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Li X, Mowlaboccus S, Jackson B, Cai C, Coombs GW. Antimicrobial Resistance Among Clinically Significant Bacteria in Wildlife: An Overlooked One Health Concern. Int J Antimicrob Agents 2024; 64:107251. [PMID: 38906487 DOI: 10.1016/j.ijantimicag.2024.107251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/30/2024] [Accepted: 06/07/2024] [Indexed: 06/23/2024]
Abstract
Antimicrobial resistance (AMR) has emerged as a critical global health challenge. However, the significance of AMR is not limited to humans and domestic animals but extends to wildlife and the environment. Based on the analysis of > 200 peer-reviewed papers, this review provides comprehensive and current insights into the detection of clinically significant antimicrobial resistant bacteria and resistance genes in wild mammals, birds and reptiles worldwide. The review also examines the overlooked roles of wildlife in AMR emergence and transmission. In wildlife, AMR is potentially driven by anthropogenic activity, agricultural and environmental factors, and natural evolution. This review highlights the significance of AMR surveillance in wildlife, identifies species and geographical foci and gaps, and demonstrates the value of multifaceted One Health strategies if further escalation of AMR globally is to be curtailed.
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Affiliation(s)
- Xing Li
- Antimicrobial Resistance and Infectious Diseases (AMRID) Research Laboratory, Harry Butler Institute, Murdoch University, Perth, Australia
| | - Shakeel Mowlaboccus
- Antimicrobial Resistance and Infectious Diseases (AMRID) Research Laboratory, Harry Butler Institute, Murdoch University, Perth, Australia; Department of Microbiology, PathWest Laboratory Medicine WA, Fiona Stanley Hospital, Perth, Australia
| | - Bethany Jackson
- School of Veterinary Medicine, Murdoch University, Perth, Australia
| | - Chang Cai
- School of Information Technology, College of Science, Technology, Engineering and Mathematics, Murdoch University, Perth, Australia
| | - Geoffrey Wallace Coombs
- Antimicrobial Resistance and Infectious Diseases (AMRID) Research Laboratory, Harry Butler Institute, Murdoch University, Perth, Australia; Department of Microbiology, PathWest Laboratory Medicine WA, Fiona Stanley Hospital, Perth, Australia.
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2
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Amábile-Cuevas CF, Lund-Zaina S. Non-Canonical Aspects of Antibiotics and Antibiotic Resistance. Antibiotics (Basel) 2024; 13:565. [PMID: 38927231 PMCID: PMC11200725 DOI: 10.3390/antibiotics13060565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/09/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024] Open
Abstract
The understanding of antibiotic resistance, one of the major health threats of our time, is mostly based on dated and incomplete notions, especially in clinical contexts. The "canonical" mechanisms of action and pharmacodynamics of antibiotics, as well as the methods used to assess their activity upon bacteria, have not changed in decades; the same applies to the definition, acquisition, selective pressures, and drivers of resistance. As a consequence, the strategies to improve antibiotic usage and overcome resistance have ultimately failed. This review gathers most of the "non-canonical" notions on antibiotics and resistance: from the alternative mechanisms of action of antibiotics and the limitations of susceptibility testing to the wide variety of selective pressures, lateral gene transfer mechanisms, ubiquity, and societal factors maintaining resistance. Only by having a "big picture" view of the problem can adequate strategies to harness resistance be devised. These strategies must be global, addressing the many aspects that drive the increasing prevalence of resistant bacteria aside from the clinical use of antibiotics.
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Affiliation(s)
| | - Sofia Lund-Zaina
- Department of Public Health, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
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3
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Dahlquist-Axe G, Standeven FJ, Speller CF, Tedder A, Meehan CJ. Inferring diet, disease and antibiotic resistance from ancient human oral microbiomes. Microb Genom 2024; 10:001251. [PMID: 38739117 PMCID: PMC11165619 DOI: 10.1099/mgen.0.001251] [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: 11/20/2023] [Accepted: 04/24/2024] [Indexed: 05/14/2024] Open
Abstract
The interaction between a host and its microbiome is an area of intense study. For the human host, it is known that the various body-site-associated microbiomes impact heavily on health and disease states. For instance, the oral microbiome is a source of various pathogens and potential antibiotic resistance gene pools. The effect of historical changes to the human host and environment to the associated microbiome, however, has been less well explored. In this review, we characterize several historical and prehistoric events which are considered to have impacted the oral environment and therefore the bacterial communities residing within it. The link between evolutionary changes to the oral microbiota and the significant societal and behavioural changes occurring during the pre-Neolithic, Agricultural Revolution, Industrial Revolution and Antibiotic Era is outlined. While previous studies suggest the functional profile of these communities may have shifted over the centuries, there is currently a gap in knowledge that needs to be filled. Biomolecular archaeological evidence of innate antimicrobial resistance within the oral microbiome shows an increase in the abundance of antimicrobial resistance genes since the advent and widespread use of antibiotics in the modern era. Nevertheless, a lack of research into the prevalence and evolution of antimicrobial resistance within the oral microbiome throughout history hinders our ability to combat antimicrobial resistance in the modern era.
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Affiliation(s)
- Gwyn Dahlquist-Axe
- School of Chemistry and Biosciences, University of Bradford, Bradford, UK
| | | | - Camilla F. Speller
- Department of Anthropology, University of British Columbia, Vancouver, Canada
| | - Andrew Tedder
- School of Chemistry and Biosciences, University of Bradford, Bradford, UK
| | - Conor J. Meehan
- Department of Biosciences, Nottingham Trent University, Nottingham, UK
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4
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Hold K, Lord E, Brealey JC, Le Moullec M, Bieker VC, Ellegaard MR, Rasmussen JA, Kellner FL, Guschanski K, Yannic G, Røed KH, Hansen BB, Dalén L, Martin MD, Dussex N. Ancient reindeer mitogenomes reveal island-hopping colonisation of the Arctic archipelagos. Sci Rep 2024; 14:4143. [PMID: 38374421 PMCID: PMC10876933 DOI: 10.1038/s41598-024-54296-2] [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: 09/25/2023] [Accepted: 02/11/2024] [Indexed: 02/21/2024] Open
Abstract
Climate warming at the end of the last glacial period had profound effects on the distribution of cold-adapted species. As their range shifted towards northern latitudes, they were able to colonise previously glaciated areas, including remote Arctic islands. However, there is still uncertainty about the routes and timing of colonisation. At the end of the last ice age, reindeer/caribou (Rangifer tarandus) expanded to the Holarctic region and colonised the archipelagos of Svalbard and Franz Josef Land. Earlier studies have proposed two possible colonisation routes, either from the Eurasian mainland or from Canada via Greenland. Here, we used 174 ancient, historical and modern mitogenomes to reconstruct the phylogeny of reindeer across its whole range and to infer the colonisation route of the Arctic islands. Our data shows a close affinity among Svalbard, Franz Josef Land and Novaya Zemlya reindeer. We also found tentative evidence for positive selection in the mitochondrial gene ND4, which is possibly associated with increased heat production. Our results thus support a colonisation of the Eurasian Arctic archipelagos from the Eurasian mainland and provide some insights into the evolutionary history and adaptation of the species to its High Arctic habitat.
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Affiliation(s)
- Katharina Hold
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Erling Skakkes Gate 47B, 7012, Trondheim, Norway.
| | - Edana Lord
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405, Stockholm, Sweden
- Department of Zoology, Stockholm University, 10691, Stockholm, Sweden
| | - Jaelle C Brealey
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Erling Skakkes Gate 47B, 7012, Trondheim, Norway
- Department of Terrestrial Ecology, Norwegian Institute of Nature Research (NINA), Høgskoleringen 9, 7034, Trondheim, Norway
| | - Mathilde Le Moullec
- Gjærevoll Centre for Biodiversity Foresight Analyses, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
- Department of Mammals and Birds, Greenland, Institute of Natural Resources, Kivioq 2, 3900, Nuuk, Greenland
| | - Vanessa C Bieker
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Erling Skakkes Gate 47B, 7012, Trondheim, Norway
| | - Martin R Ellegaard
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Erling Skakkes Gate 47B, 7012, Trondheim, Norway
| | - Jacob A Rasmussen
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Erling Skakkes Gate 47B, 7012, Trondheim, Norway
- Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | - Fabian L Kellner
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Erling Skakkes Gate 47B, 7012, Trondheim, Norway
| | - Katerina Guschanski
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Glenn Yannic
- Univ. Savoie Mont Blanc, CNRS, LECA, Laboratoire d'Ecologie Alpine, Univ. Grenoble Alpes, 38000, Grenoble, France
| | - Knut H Røed
- Department of Preclinical Sciences and Pathology, Norwegian University of Life Sciences, P.O. Box 5003, 1432, Ås, Norway
| | - Brage B Hansen
- Gjærevoll Centre for Biodiversity Foresight Analyses, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
- Department of Terrestrial Ecology, Norwegian Institute of Nature Research (NINA), Høgskoleringen 9, 7034, Trondheim, Norway
| | - Love Dalén
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405, Stockholm, Sweden
- Department of Zoology, Stockholm University, 10691, Stockholm, Sweden
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Erling Skakkes Gate 47B, 7012, Trondheim, Norway.
| | - Nicolas Dussex
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Erling Skakkes Gate 47B, 7012, Trondheim, Norway.
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5
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Fiorin E, Roberts CA, Baldoni M, Connelly E, Lee C, Ottoni C, Cristiani E. First archaeological evidence for ginger consumption as a potential medicinal ingredient in a late medieval leprosarium at St Leonard, Peterborough, England. Sci Rep 2024; 14:2452. [PMID: 38291078 PMCID: PMC10827753 DOI: 10.1038/s41598-024-52422-8] [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: 01/18/2024] [Indexed: 02/01/2024] Open
Abstract
Leprosy was one of the most outwardly visible diseases in the European Middle Ages, a period during which leprosaria were founded to provide space for the sick. The extant documentary evidence for leprosy hospitals, especially in relation to diet, therapeutic, and medical care, is limited. However, human dental calculus stands to be an important source of information as it provides insight into the substances people were exposed to and accumulated in their bodies during their lives. In the present study, microremains and DNA were analysed from the calculus of individuals buried in the late medieval cemetery of St Leonard, a leprosarium located in Peterborough, England. The results show the presence of ginger (Zingiber officinale), a culinary and medicinal ingredient, as well as evidence of consumption of cereals and legumes. This research suggests that affected individuals consumed ingredients mentioned in medieval medical textbooks that were used to treat regions of the body typically impacted by leprosy. To the authors' knowledge, this is the first study which has identified Zingiber officinale in human dental calculus in England or on the wider European continent.
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Affiliation(s)
- Elena Fiorin
- Department of Oral and Maxillofacial Sciences, DANTE-Diet and Ancient Technology Laboratory, Sapienza University of Rome, 00161, Rome, Italy.
| | - Charlotte A Roberts
- Department of Archaeology, Durham University, Durham, DH1 3LE, United Kingdom
| | - Marica Baldoni
- Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Erin Connelly
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Christina Lee
- School of English, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Claudio Ottoni
- Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Emanuela Cristiani
- Department of Oral and Maxillofacial Sciences, DANTE-Diet and Ancient Technology Laboratory, Sapienza University of Rome, 00161, Rome, Italy
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6
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Grasso G, Bianciotto V, Marmeisse R. Paleomicrobiology: Tracking the past microbial life from single species to entire microbial communities. Microb Biotechnol 2024; 17:e14390. [PMID: 38227345 PMCID: PMC10832523 DOI: 10.1111/1751-7915.14390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 11/04/2023] [Accepted: 12/10/2023] [Indexed: 01/17/2024] Open
Abstract
By deciphering information encoded in degraded ancient DNA extracted from up to million-years-old samples, molecular paleomicrobiology enables to objectively retrace the temporal evolution of microbial species and communities. Assembly of full-length genomes of ancient pathogen lineages allows not only to follow historical epidemics in space and time but also to identify the acquisition of genetic features that represent landmarks in the evolution of the host-microbe interaction. Analysis of microbial community DNA extracted from essentially human paleo-artefacts (paleofeces, dental calculi) evaluates the relative contribution of diet, lifestyle and geography on the taxonomic and functional diversity of these guilds in which have been identified species that may have gone extinct in today's human microbiome. As for non-host-associated environmental samples, such as stratified sediment cores, analysis of their DNA illustrates how and at which pace microbial communities are affected by local or widespread environmental disturbance. Description of pre-disturbance microbial diversity patterns can aid in evaluating the relevance and effectiveness of remediation policies. We finally discuss how recent achievements in paleomicrobiology could contribute to microbial biotechnology in the fields of medical microbiology and food science to trace the domestication of microorganisms used in food processing or to illustrate the historic evolution of food processing microbial consortia.
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Affiliation(s)
- Gianluca Grasso
- Dipartimento di Scienze della Vita e Biologia dei SistemiUniversità degli Studi of TurinTurinItaly
- Institut Systématique Evolution, Biodiversité (ISYEB: UMR7205 CNRS‐MNHN‐Sorbonne Université‐EPHE‐UA)¸ Muséum National d'Histoire NaturelleParisFrance
- Institute for Sustainable Plant Protection (IPSP), SSNational Research Council (CNR)TurinItaly
| | - Valeria Bianciotto
- Institute for Sustainable Plant Protection (IPSP), SSNational Research Council (CNR)TurinItaly
| | - Roland Marmeisse
- Institut Systématique Evolution, Biodiversité (ISYEB: UMR7205 CNRS‐MNHN‐Sorbonne Université‐EPHE‐UA)¸ Muséum National d'Histoire NaturelleParisFrance
- Institute for Sustainable Plant Protection (IPSP), SSNational Research Council (CNR)TurinItaly
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7
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Rayfield KM, Mychajliw AM, Singleton RR, Sholts SB, Hofman CA. Uncovering the Holocene roots of contemporary disease-scapes: bringing archaeology into One Health. Proc Biol Sci 2023; 290:20230525. [PMID: 38052246 DOI: 10.1098/rspb.2023.0525] [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: 04/03/2023] [Accepted: 11/06/2023] [Indexed: 12/07/2023] Open
Abstract
The accelerating pace of emerging zoonotic diseases in the twenty-first century has motivated cross-disciplinary collaboration on One Health approaches, combining microbiology, veterinary and environmental sciences, and epidemiology for outbreak prevention and mitigation. Such outbreaks are often caused by spillovers attributed to human activities that encroach on wildlife habitats and ecosystems, such as land use change, industrialized food production, urbanization and animal trade. While the origin of anthropogenic effects on animal ecology and biogeography can be traced to the Late Pleistocene, the archaeological record-a long-term archive of human-animal-environmental interactions-has largely been untapped in these One Health approaches, thus limiting our understanding of these dynamics over time. In this review, we examine how humans, as niche constructors, have facilitated new host species and 'disease-scapes' from the Late Pleistocene to the Anthropocene, by viewing zooarchaeological, bioarchaeological and palaeoecological data with a One Health perspective. We also highlight how new biomolecular tools and advances in the '-omics' can be holistically coupled with archaeological and palaeoecological reconstructions in the service of studying zoonotic disease emergence and re-emergence.
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Affiliation(s)
- Kristen M Rayfield
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
- Laboratories of Molecular Anthropology & Microbiome Research, University of Oklahoma, Norman, OK, USA
- Department of Anthropology, University of Oklahoma, Norman, OK 73019-0390, USA
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Alexis M Mychajliw
- Laboratories of Molecular Anthropology & Microbiome Research, University of Oklahoma, Norman, OK, USA
- Department of Anthropology, University of Oklahoma, Norman, OK 73019-0390, USA
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- Department of Biology & Program in Environmental Studies, Middlebury College, Middlebury, VT 05753-6203, USA
| | - Robin R Singleton
- Laboratories of Molecular Anthropology & Microbiome Research, University of Oklahoma, Norman, OK, USA
- Department of Anthropology, University of Oklahoma, Norman, OK 73019-0390, USA
| | - Sabrina B Sholts
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Courtney A Hofman
- Laboratories of Molecular Anthropology & Microbiome Research, University of Oklahoma, Norman, OK, USA
- Department of Anthropology, University of Oklahoma, Norman, OK 73019-0390, USA
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
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8
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Michel A, Minocher R, Niehoff PP, Li Y, Nota K, Gadhvi MA, Su J, Iyer N, Porter A, Ngobobo-As-Ibungu U, Binyinyi E, Nishuli Pekeyake R, Parducci L, Caillaud D, Guschanski K. Isolated Grauer's gorilla populations differ in diet and gut microbiome. Mol Ecol 2023; 32:6523-6542. [PMID: 35976262 DOI: 10.1111/mec.16663] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 08/09/2022] [Accepted: 08/11/2022] [Indexed: 11/30/2022]
Abstract
The animal gut microbiome has been implicated in a number of key biological processes, ranging from digestion to behaviour, and has also been suggested to facilitate local adaptation. Yet studies in wild animals rarely compare multiple populations that differ ecologically, which is the level at which local adaptation may occur. Further, few studies simultaneously characterize diet and gut microbiome from the same sample, despite their probable interdependence. Here, we investigate the interplay between diet and gut microbiome in three geographically isolated populations of the critically endangered Grauer's gorilla (Gorilla beringei graueri), which we show to be genetically differentiated. We find population- and social group-specific dietary and gut microbial profiles and covariation between diet and gut microbiome, despite the presence of core microbial taxa. There was no detectable effect of age, and only marginal effects of sex and genetic relatedness on the microbiome. Diet differed considerably across populations, with the high-altitude population consuming a lower diversity of plants compared to low-altitude populations, consistent with plant availability constraining dietary choices. The observed pattern of covariation between diet and gut microbiome is probably a result of long-term social and environmental factors. Our study suggests that the gut microbiome is sufficiently plastic to support flexible food selection and hence contribute to local adaptation.
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Affiliation(s)
- Alice Michel
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
- Department of Anthropology, University of California, Davis, California, USA
| | - Riana Minocher
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
- Department of Human Behavior, Ecology and Culture, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Peter-Philip Niehoff
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Yuhong Li
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
- Conservation Ecology Group, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Kevin Nota
- Plant Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Maya A Gadhvi
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Jiancheng Su
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Neetha Iyer
- Department of Anthropology, University of California, Davis, California, USA
| | - Amy Porter
- Department of Anthropology, University of California, Davis, California, USA
| | | | - Escobar Binyinyi
- The Dian Fossey Gorilla Fund International, Kinshasa, Democratic Republic of the Congo
| | - Radar Nishuli Pekeyake
- Institut Congolais pour la Conservation de la Nature, Kinshasa, Democratic Republic of the Congo
| | - Laura Parducci
- Department of Human Behavior, Ecology and Culture, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
| | - Damien Caillaud
- Department of Anthropology, University of California, Davis, California, USA
| | - Katerina Guschanski
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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9
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Huang G, Shi W, Wang L, Qu Q, Zuo Z, Wang J, Zhao F, Wei F. PandaGUT provides new insights into bacterial diversity, function, and resistome landscapes with implications for conservation. MICROBIOME 2023; 11:221. [PMID: 37805557 PMCID: PMC10559513 DOI: 10.1186/s40168-023-01657-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 08/23/2023] [Indexed: 10/09/2023]
Abstract
BACKGROUND The gut microbiota play important roles in host adaptation and evolution, but are understudied in natural population of wild mammals. To address host adaptive evolution and improve conservation efforts of threatened mammals from a metagenomic perspective, we established a high-quality gut microbiome catalog of the giant panda (pandaGUT) to resolve the microbiome diversity, functional, and resistome landscapes using approximately 7 Tbp of long- and short-read sequencing data from 439 stool samples. RESULTS The pandaGUT catalog comprises 820 metagenome-assembled genomes, including 40 complete closed genomes, and 64.5% of which belong to species that have not been previously reported, greatly expanding the coverage of most prokaryotic lineages. The catalog contains 2.37 million unique genes, with 74.8% possessing complete open read frames, facilitating future mining of microbial functional potential. We identified three microbial enterotypes across wild and captive panda populations characterized by Clostridium, Pseudomonas, and Escherichia, respectively. We found that wild pandas exhibited host genetic-specific microbial structures and functions, suggesting host-gut microbiota phylosymbiosis, while the captive cohorts encoded more multi-drug resistance genes. CONCLUSIONS Our study provides largely untapped resources for biochemical and biotechnological applications as well as potential intervention avenues via the rational manipulation of microbial diversity and reducing antibiotic usage for future conservation management of wildlife. Video Abstract.
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Affiliation(s)
- Guangping Huang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wenyu Shi
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Le Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qingyue Qu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhenqiang Zuo
- Laboratory for Computational Genomics, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jinfeng Wang
- Laboratory for Computational Genomics, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fangqing Zhao
- Laboratory for Computational Genomics, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Fuwen Wei
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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10
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Pinnell LJ, Kuiper G, Huebner KL, Doster E, Parker JK, Alekozai N, Powers JG, Wallen RL, Belk KE, Morley PS. More than an anthropogenic phenomenon: Antimicrobial resistance in ungulates from natural and agricultural environments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 858:159789. [PMID: 36309273 DOI: 10.1016/j.scitotenv.2022.159789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/24/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
Widely considered an anthropogenic phenomenon, antimicrobial resistance (AMR) is a naturally occurring mechanism that microorganisms use to gain competitive advantage. AMR represents a significant threat to public health and has generated criticism towards the overuse of antimicrobial drugs. Livestock have been proposed as important reservoirs for AMR accumulation. Here, we show that assemblages of AMR genes in cattle and ungulates from natural environments (Yellowstone and Rocky Mountain National Parks) are all dominated by genes conferring resistance to tetracyclines. However, cattle feces contained higher proportions of erm(A-X) genes conferring resistance to macrolide antibiotics. Medically important AMR genes differed between cattle and natural ungulates, but cumulatively were more predominant in natural soils. Our findings suggest that the commonly described predominance of tetracycline resistance in cattle feces is a natural phenomenon among multiple ungulate species and not solely a result of antimicrobial drug exposure. Yet, the virtual absence of macrolide resistance genes in natural ungulates suggests that macrolide usage in agriculture may enrich these genes in cattle. Our results show that antimicrobial use in agriculture may be promoting a potential reservoir for specific types of AMR (i.e., macrolide resistance) but that a significant proportion of the ungulate resistome appears to have natural origins.
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Affiliation(s)
- Lee J Pinnell
- Veterinary Education, Research, and Outreach Program, Texas A&M University, Canyon, TX 79015, USA
| | - Grace Kuiper
- Colorado State University, Fort Collins, CO 80523, USA
| | | | - Enrique Doster
- Veterinary Education, Research, and Outreach Program, Texas A&M University, Canyon, TX 79015, USA; Colorado State University, Fort Collins, CO 80523, USA
| | | | | | - Jenny G Powers
- Biological Resources Division, National Park Service, Fort Collins, CO 80521, USA
| | - Rick L Wallen
- Yellowstone National Park, National Park Service, Mammoth, WY 82190, USA
| | - Keith E Belk
- Colorado State University, Fort Collins, CO 80523, USA
| | - Paul S Morley
- Veterinary Education, Research, and Outreach Program, Texas A&M University, Canyon, TX 79015, USA.
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Moraitou M, Forsythe A, Fellows Yates JA, Brealey JC, Warinner C, Guschanski K. Ecology, Not Host Phylogeny, Shapes the Oral Microbiome in Closely Related Species. Mol Biol Evol 2022; 39:6874787. [PMID: 36472532 PMCID: PMC9778846 DOI: 10.1093/molbev/msac263] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 11/25/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
Host-associated microbiomes are essential for a multitude of biological processes. Placed at the contact zone between external and internal environments, the little-studied oral microbiome has important roles in host physiology and health. Here, we investigate the roles of host evolutionary relationships and ecology in shaping the oral microbiome in three closely related gorilla subspecies (mountain, Grauer's, and western lowland gorillas) using shotgun metagenomics of 46 museum-preserved dental calculus samples. We find that the oral microbiomes of mountain gorillas are functionally and taxonomically distinct from the other two subspecies, despite close evolutionary relationships and geographic proximity with Grauer's gorillas. Grauer's gorillas show intermediate bacterial taxonomic and functional, and dietary profiles. Altitudinal differences in gorilla subspecies ranges appear to explain these patterns, suggesting a close connection between dental calculus microbiomes and the environment, likely mediated through diet. This is further supported by the presence of gorilla subspecies-specific phyllosphere/rhizosphere taxa in the oral microbiome. Mountain gorillas show a high abundance of nitrate-reducing oral taxa, which may promote adaptation to a high-altitude lifestyle by modulating blood pressure. Our results suggest that ecology, rather than evolutionary relationships and geographic distribution, shape the oral microbiome in these closely related species.
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Affiliation(s)
| | | | - James A Fellows Yates
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany,Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, 07745 Jena, Germany
| | - Jaelle C Brealey
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany,Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, 07745 Jena, Germany,Faculty of Biological Sciences, Friedrich Schiller University, 07743 Jena, Germany,Department of Anthropology, Harvard University, Cambridge, MA 02138, USA
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Attitudes towards Use of High-Importance Antimicrobials—A Cross-Sectional Study of Australian Veterinarians. Antibiotics (Basel) 2022; 11:antibiotics11111589. [DOI: 10.3390/antibiotics11111589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 11/12/2022] Open
Abstract
The timely implementation of antimicrobial stewardship interventions could delay or prevent the development of higher levels of antimicrobial resistance in the future. In food-producing animals in Australia, high-importance antimicrobials, as rated by the Australian Strategic and Technical Advisory Group (ASTAG), include virginiamycin and third-generation cephalosporins (in individual pigs or cattle). The use of high-importance antimicrobials in companion animals is more widespread and less regulated. There is no national antimicrobial use surveillance system for animals in Australia. Consequently, there is a gap in the knowledge about reasonable use across all sectors of veterinary practice. This study explored attitudes towards the use in veterinary medicine of antimicrobials with high importance to human health, and determined levels of agreement about the introduction of restrictions or other conditions on this use. An online survey was distributed via social media and email from June to December 2020 to veterinarians working in Australia. Of the 278 respondents working in clinical practice, 49% had heard of the ASTAG rating system, and 22% used a traffic light system for antimicrobial importance in their practice. Overall, 61% of participants disagreed that veterinarians should be able to prescribe high-importance antimicrobials without restrictions. If there were to be restrictions, there was most agreement amongst all respondents for only restricting high-importance antimicrobials (73%). There is a need for education, guidance, and practical support for veterinarians for prescribing high-importance antimicrobials alongside any restrictions.
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A bottom-up view of antimicrobial resistance transmission in developing countries. Nat Microbiol 2022; 7:757-765. [PMID: 35637328 DOI: 10.1038/s41564-022-01124-w] [Citation(s) in RCA: 75] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 04/11/2022] [Indexed: 12/15/2022]
Abstract
Antimicrobial resistance (AMR) is tracked most closely in clinical settings and high-income countries. However, resistant organisms thrive globally and are transmitted to and from healthy humans, animals and the environment, particularly in many low- and middle-income settings. The overall public health and clinical significance of these transmission opportunities remain to be completely clarified. There is thus considerable global interest in promoting a One Health view of AMR to enable a more realistic understanding of its ecology. In reality, AMR surveillance outside hospitals remains insufficient and it has been very challenging to convincingly document transmission at the interfaces between clinical specimens and other niches. In this Review, we describe AMR and its transmission in low- and middle-income-country settings, emphasizing high-risk transmission points such as urban settings and food-animal handling. In urban and food production settings, top-down and infrastructure-dependent interventions against AMR that require strong regulatory oversight are less likely to curtail transmission when used alone and should be combined with bottom-up AMR-containment approaches. We observe that the power of genomics to expose transmission channels and hotspots is largely unharnessed, and that existing and upcoming technological innovations need to be exploited towards containing AMR in low- and middle-income settings.
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Ramey AM. Antimicrobial resistance: Wildlife as indicators of anthropogenic environmental contamination across space and through time. Curr Biol 2021; 31:R1385-R1387. [PMID: 34699802 DOI: 10.1016/j.cub.2021.08.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Prior assessments support wildlife as indicators of anthropogenically influenced antimicrobial resistance across the landscape. A ground-breaking new study suggests that wildlife may also provide information on antimicrobial resistance in the environment through time.
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Affiliation(s)
- Andrew M Ramey
- US Geological Survey Alaska Science Center, Anchorage, AK 99508, USA.
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