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Blanco-Peña K, Quesada-Alvarado F, Salas-González D, Estrada-König S, Salom-Pérez R, Arroyo-Arce S, Villalobos-Araya A, Rivera-Castillo J, Martín-Maldonado B, Corrales-Gutiérrez D, Gallardo-Castro V, Gutiérrez-Espeleta G, Chaves A, Esperón F, Chaverri-Fonseca F. A multidisciplinary approach to analyze the antimicrobial resistance in natural ecosystems. ENVIRONMENTAL RESEARCH 2024; 251:118549. [PMID: 38412915 DOI: 10.1016/j.envres.2024.118549] [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: 12/26/2023] [Revised: 02/07/2024] [Accepted: 02/23/2024] [Indexed: 02/29/2024]
Abstract
Antimicrobial Resistance (AMR) poses a global threat to both human health and environmental well-being. Our study delved into Costa Rican wildlife reserves, uncovering a substantial human impact on these ecosystems and underscoring the imperative to pinpoint AMR hotspots. Embracing a One Health perspective, we advocated for a comprehensive landscape analysis that intricately intertwined geographic, climatic, forest, and human factors. This study illuminated the link between laboratory results and observed patterns of antimicrobial use, thereby paving the way for sustainable solutions. Our innovative methodology involved deploying open-ended questions to explore antimicrobial usage across livestock activities, contributing to establishing a comprehensive methodology. Non-invasive sampling in wildlife emerged as a critical aspect, shedding light on areas contaminated by AMR. Feline species, positioned at the apex of the food chain, acted as sentinels for environmental health due to heightened exposure to improperly disposed waste. Regarding laboratory findings, each sample revealed the presence of at least one antimicrobial resistance gene (ARG). Notably, genes encoding resistance to tetracyclines dominated (94.9%), followed by beta-lactams (75.6%), sulfonamides (53.8%), aminoglycosides (51.3%), quinolones (44.9%), phenicols (25.6%), and macrolides (20.5%). Genes encoding polymyxins were not detected. Moreover, 66% of samples carried a multi-resistant microbiome, with 15% exhibiting resistance to three antimicrobial families and 51% to four. The absence of a correlation between forest coverage and ARG presence underscored the profound human impact on wildlife reserves, surpassing previous estimations. This environmental pressure could potentially modify microbiomes and resistomes in unknown ways. As not all antimicrobial families encoding ARGs were utilized by farmers, our next step involved evaluating other human activities to identify the primary sources of contamination. This comprehensive study contributed crucial insights into the intricate dynamics of AMR in natural ecosystems, paving the way for targeted interventions and sustainable coexistence.
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Affiliation(s)
- Kinndle Blanco-Peña
- Universidad Nacional, Costa Rica. Instituto Regional de Estudios en Sustancias Tóxicas (IRET), Costa Rica.
| | - Francisco Quesada-Alvarado
- Universidad Nacional, Costa Rica. Instituto Regional de Estudios en Sustancias Tóxicas (IRET), Costa Rica
| | - Denis Salas-González
- Universidad Nacional, Costa Rica. Instituto Regional de Estudios en Sustancias Tóxicas (IRET), Costa Rica
| | | | | | | | | | | | - Bárbara Martín-Maldonado
- Veterinary Department, School of Biomedical and Health Sciences, Universidad Europea de Madrid, Spain
| | | | | | | | - Andrea Chaves
- School of Biology, Universidad de Costa Rica, San Pedro, Costa Rica
| | - Fernando Esperón
- Veterinary Department, School of Biomedical and Health Sciences, Universidad Europea de Madrid, Spain
| | - Fabio Chaverri-Fonseca
- Universidad Nacional, Costa Rica. Instituto Regional de Estudios en Sustancias Tóxicas (IRET), Costa Rica
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Vargas-Villalobos S, Hernández F, Fabregat-Safont D, Salas-González D, Quesada-Alvarado F, Botero-Coy AM, Esperón F, Martín-Maldonado B, Monrós-Gonzalez J, Ruepert C, Estrada-König S, Rivera-Castillo J, Chaverri-Fonseca F, Blanco-Peña K. A case study on pharmaceutical residues and antimicrobial resistance genes in Costa Rican rivers: A possible route of contamination for feline and other species. ENVIRONMENTAL RESEARCH 2024; 242:117665. [PMID: 37993051 DOI: 10.1016/j.envres.2023.117665] [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: 09/12/2023] [Revised: 11/08/2023] [Accepted: 11/12/2023] [Indexed: 11/24/2023]
Abstract
In this investigation, the presence of antibiotics and pharmaceuticals in Costa Rican surface waters, specifically in regions near feline habitats, was examined. The study revealed that 47% of the water samples contained detectable traces of at least one antibiotic. Ciprofloxacin and norfloxacin were the most frequently detected compounds, each with a detection rate of 27%. Other antibiotics, such as erythromycin, roxithromycin, and trimethoprim, were also found but at lower frequencies, around 14%. Notably, all antibiotic concentrations remained below 10 ng/L, with ciprofloxacin, norfloxacin, and erythromycin showing the highest concentrations. Furthermore, the investigation revealed the presence of non-antibiotic pharmaceutical residues in the water samples, typically at concentrations below 64 ng/L. Tramadol was the most frequently detected compound, present in 18% of the samples. The highest concentrations were observed for acetaminophen and tramadol, measuring 64 and 10 ng/L, respectively. Comparing these findings with studies conducted in treated wastewater and urban rivers, it became evident that the concentrations of antibiotics and pharmaceuticals were notably lower in this study. While previous research reported higher values, the limited number of studies conducted in protected areas raises concerns about the potential environmental impact on biodiversity. In summary, these results emphasize the importance of monitoring pharmaceutical residues and antimicrobial resistance genes ARGs in vulnerable ecosystems, especially those in close proximity to feline habitats in Costa Rica. Additionally, the study delved into the detection of (ARGs). All tested water samples were positive for at least one ARG, with the blaTEM gene being the most prevalent at 82%, followed by tetS at 64% and qnrB at 23%. Moreover, this research shed light on the complexity of evaluating ARGs in environmental samples, as their presence does not necessarily indicate their expression. It also highlighted the potential for co-selection and co-regulation of ARGs, showcasing the intricate behaviors of these genes in aquatic environments.
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Affiliation(s)
- Seiling Vargas-Villalobos
- Universidad Nacional, Instituto Regional de Estudios en Sustancias Tóxicas, (IRET), 86-3000, Heredia, Costa Rica; Doctoral Program in Pollution, Toxicology and Environmental Health Universitat de València, España Av. Blasco Ibáñez, 13.46010, Valencia, Spain.
| | - Félix Hernández
- Environmental and Public Health Analytical Chemistry, Research Institute for Pesticides and Water, University Jaume I, Avda. Sos Baynat S/n, 12071, Castelló, Spain
| | - David Fabregat-Safont
- Environmental and Public Health Analytical Chemistry, Research Institute for Pesticides and Water, University Jaume I, Avda. Sos Baynat S/n, 12071, Castelló, Spain; Applied Metabolomics Research Laboratory, IMIM-Hospital Del Mar Medical Research Institute, 88 Doctor Aiguader, 08003, Barcelona, Spain
| | - Denis Salas-González
- Universidad Nacional, Instituto Regional de Estudios en Sustancias Tóxicas, (IRET), 86-3000, Heredia, Costa Rica
| | - Francisco Quesada-Alvarado
- Universidad Nacional, Instituto Regional de Estudios en Sustancias Tóxicas, (IRET), 86-3000, Heredia, Costa Rica
| | - Ana Maria Botero-Coy
- Environmental and Public Health Analytical Chemistry, Research Institute for Pesticides and Water, University Jaume I, Avda. Sos Baynat S/n, 12071, Castelló, Spain
| | - Fernando Esperón
- Veterinary Department, School of Biomedical and Health Sciences, Universidad Europea de Madrid, Spain
| | - Bárbara Martín-Maldonado
- Veterinary Department, School of Biomedical and Health Sciences, Universidad Europea de Madrid, Spain
| | - Juan Monrós-Gonzalez
- Institut "Cavanilles" de Biodiversitat I Biologia Evolutiva Universitat de València, Spain
| | - Clemens Ruepert
- Universidad Nacional, Instituto Regional de Estudios en Sustancias Tóxicas, (IRET), 86-3000, Heredia, Costa Rica
| | - Sandra Estrada-König
- Universidad Nacional. Escuela de Medicina Veterinaria, 86-3000, Heredia, Costa Rica
| | | | - Fabio Chaverri-Fonseca
- Universidad Nacional, Instituto Regional de Estudios en Sustancias Tóxicas, (IRET), 86-3000, Heredia, Costa Rica
| | - Kinndle Blanco-Peña
- Universidad Nacional, Instituto Regional de Estudios en Sustancias Tóxicas, (IRET), 86-3000, Heredia, Costa Rica
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Rohrer SD, Jiménez-Uzcátegui G, Parker PG, Chubiz LM. Composition and function of the Galapagos penguin gut microbiome vary with age, location, and a putative bacterial pathogen. Sci Rep 2023; 13:5358. [PMID: 37005428 PMCID: PMC10067942 DOI: 10.1038/s41598-023-31826-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 03/17/2023] [Indexed: 04/04/2023] Open
Abstract
Microbial colonization plays a direct role in host health. Understanding the ecology of the resident microbial community for a given host species is thus an important step for detecting population vulnerabilities like disease. However, the idea of integrating microbiome research into conservation is still relatively new, and wild birds have received less attention in this field than mammals or domesticated animals. Here we examine the composition and function of the gut microbiome of the endangered Galapagos penguin (Spheniscus mendiculus) with the goals of characterizing the normal microbial community and resistome, identifying likely pathogens, and testing hypotheses of structuring forces for this community based on demographics, location, and infection status. We collected fecal samples from wild penguins in 2018 and performed 16S rRNA gene sequencing and whole genome sequencing (WGS) on extracted DNA. 16S sequencing revealed that the bacterial phyla Fusobacteria, Epsilonbacteraeota, Firmicutes, and Proteobacteria dominate the community. Functional pathways were computed from WGS data, showing genetic functional potential primarily focused on metabolism-amino acid metabolism, carbohydrate metabolism, and energy metabolism are the most well-represented functional groups. WGS samples were each screened for antimicrobial resistance, characterizing a resistome made up of nine antibiotic resistance genes. Samples were screened for potential enteric pathogens using virulence factors as indicators; Clostridium perfringens was revealed as a likely pathogen. Overall, three factors appear to be shaping the alpha and beta diversity of the microbial community: penguin developmental stage, sampling location, and C. perfringens. We found that juvenile penguins have significantly lower alpha diversity than adults based on three metrics, as well as significantly different beta diversity. Location effects are minimal, but one site has significantly lower Shannon diversity than the other primary sites. Finally, when samples were grouped by C. perfringens virulence factors, we found dramatic changes in beta diversity based on operational taxonomic units, protein families, and functional pathways. This study provides a baseline microbiome for an endangered species, implicates both penguin age and the presence of a potential bacterial pathogen as primary factors associated with microbial community variance, and reveals widespread antibiotic resistance genes across the population.
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Affiliation(s)
- Sage D Rohrer
- Department of Biology and Whitney R. Harris World Ecology Center, University of Missouri-St. Louis, One University Blvd., St. Louis, MO, 63121, USA.
| | | | - Patricia G Parker
- Department of Biology and Whitney R. Harris World Ecology Center, University of Missouri-St. Louis, One University Blvd., St. Louis, MO, 63121, USA
- WildCare Institute, Saint Louis Zoo, One Government Drive, St. Louis, MO, 63110, USA
| | - Lon M Chubiz
- Department of Biology and Whitney R. Harris World Ecology Center, University of Missouri-St. Louis, One University Blvd., St. Louis, MO, 63121, USA
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Mengistu TS, Garcias B, Castellanos G, Seminati C, Molina-López RA, Darwich L. Occurrence of multidrug resistant Gram-negative bacteria and resistance genes in semi-aquatic wildlife - Trachemys scripta, Neovison vison and Lutra lutra - as sentinels of environmental health. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 830:154814. [PMID: 35341839 DOI: 10.1016/j.scitotenv.2022.154814] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 03/20/2022] [Accepted: 03/21/2022] [Indexed: 06/14/2023]
Abstract
Emergence of antimicrobial resistance (AMR) in bacterial pathogens has been recognized as a major public health concern worldwide. In the present study, antimicrobial resistant Gram-negative bacteria (AMRGNB) and AMR genes were assessed in semi-aquatic wild animals from a highly populated and intensive farming region of Spain, Catalonia. Cloacal/rectal swab samples were collected from 241 animals coming from invasive species Trachemys scripta (n = 91) and Neovison vison (n = 131), and endangered-protected species Lutra lutra (n = 19). Accordingly, 133 (55.2%) isolates were identified as AMRGNB. Escherichia coli and Pseudomonas fluorescens were among the bacteria most frequently isolated in all animal species, but other nosocomial agents such as Klebsiella pneumoniae, Salmonella spp. or Citrobacter freundii, were also prevalent. The phenotypic susceptibility testing showed the highest resistance to β-lactams (91%). Molecular analysis showed 25.3% of turtles (15.4% ESBL/Ampc genes), 21% of Eurasian otters (10.5% ESBL/Ampc genes) and 14.5% of American minks (8.4% ESBL/Ampc genes) were positive to AMR genes. The genotyping frequency was tetM (20.6%), blaCMY-2 (13%), ermB (6.1%), blaCMY-1 (4.6%), blaCTX-M-15 (3.1%) and mcr-4 (0.8%). Turtles had a larger prevalence of AMRGNB and AMR genes than mustelids, but American mink carried mcr-4 colistin-resistance gene. Moreover, cluster analysis of AMR gene distribution revealed that an ESBL/AmpC cluster in a highly populated area comprising big metropolitan regions, and another tetM/emrB cluster in an expended area with highly intensive livestock production. Although the mcr-4 positive case was not included in those clusters, that case was found in a county with a high pig farm density. In conclusion, semi-aquatic wild animals are a good sentinel for environmental contamination with AMRGNB and AMR genes. Therefore, One Health Approach is urgently needed in highly populated regions, and with intensive livestock production like Catalonia.
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Affiliation(s)
| | - Biel Garcias
- Department Sanitat i Anatomia Animals, Veterinary Faculty, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, CP 08193, Spain.
| | - Gabriela Castellanos
- Department Sanitat i Anatomia Animals, Veterinary Faculty, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, CP 08193, Spain.
| | - Chiara Seminati
- Department Sanitat i Anatomia Animals, Veterinary Faculty, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, CP 08193, Spain.
| | | | - Laila Darwich
- Department Sanitat i Anatomia Animals, Veterinary Faculty, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, CP 08193, Spain.
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Nieto-Claudin A, Deem SL, Rodríguez C, Cano S, Moity N, Cabrera F, Esperón F. Antimicrobial resistance in Galapagos tortoises as an indicator of the growing human footprint. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 284:117453. [PMID: 34090252 DOI: 10.1016/j.envpol.2021.117453] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 06/12/2023]
Abstract
Antimicrobial resistance has become one of the main public health threats worldwide with anthropogenic activities driving the spread of resistance. Understanding and combatting the spread of resistant bacteria is a top priority for global health institutions, and it is included as one of the main goals of the One Health initiative. Giant tortoises (Chelonoidis spp.), some of the most iconic species on Earth, are widely distributed across the Galapagos archipelago and are thus perfect candidates to test the hypothesis that wildlife species in the Galapagos carry antimicrobial resistant genes (ARGs) associated with human activities. We sampled a total of 200 free-living Galapagos tortoises from western Santa Cruz Island (C. porteri), the most human-populated island of the archipelago, and 70 tortoises (C. vandenburghi) from the isolated Alcedo Volcano on Isabela Island, a natural area with minimal human presence. Fecal samples were analyzed by quantitative PCR for a panel of 21 ARGs conferring resistance for eight antimicrobial classes. We found ARGs in both Santa Cruz and Alcedo Volcano giant tortoises; however, both qualitative and quantitative results showed higher loads of ARGs in tortoises inhabiting the human modified environments of Santa Cruz. Moreover, Santa Cruz tortoises sampled in higher human-modified landscapes (i.e., farmlands and urban areas) presented a higher number of ARGs, antimicrobial classes, and multi-resistant microbiomes than those from less anthropized areas within the same island. Our findings suggest that human activities in Galapagos have a negative impact on ecosystem health through ARG dispersal. This research highlights a new threat for the health and conservation of the unique wildlife of the Galapagos, their ecosystems, and the humans inhabiting this World Heritage Site. Our recommendation to local policy makers is to control and reduce the use of antibiotics in both human and animal health, thus helping enforce antimicrobial regulations.
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Affiliation(s)
- Ainoa Nieto-Claudin
- Charles Darwin Research Station, Charles Darwin Foundation, Santa Cruz, Galapagos, Ecuador; Complutense University of Madrid, Veterinary Faculty, Puerta de Hierro Av, Madrid, 28040. Spain; Saint Louis Zoo Institute for Conservation Medicine, One Government Drive, Saint Louis, MO, 63110. USA.
| | - Sharon L Deem
- Charles Darwin Research Station, Charles Darwin Foundation, Santa Cruz, Galapagos, Ecuador; Saint Louis Zoo Institute for Conservation Medicine, One Government Drive, Saint Louis, MO, 63110. USA.
| | - Casilda Rodríguez
- Complutense University of Madrid, Veterinary Faculty, Puerta de Hierro Av, Madrid, 28040. Spain.
| | - Santiago Cano
- Complutense University of Madrid, Veterinary Faculty, Puerta de Hierro Av, Madrid, 28040. Spain.
| | - Nicolas Moity
- Charles Darwin Research Station, Charles Darwin Foundation, Santa Cruz, Galapagos, Ecuador.
| | - Freddy Cabrera
- Charles Darwin Research Station, Charles Darwin Foundation, Santa Cruz, Galapagos, Ecuador.
| | - Fernando Esperón
- Complutense University of Madrid, Veterinary Faculty, Puerta de Hierro Av, Madrid, 28040. Spain; INIA-CISA. Algete-El Casar Road, Valdeolmos, 28130. Spain.
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Body size, sex and high philopatry influence the use of agricultural land by Galapagos giant tortoises. ORYX 2021. [DOI: 10.1017/s0030605320001167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
AbstractAs agricultural areas expand, interactions between wild animals and farmland are increasing. Understanding the nature of such interactions is vital to inform the management of human–wildlife coexistence. We investigated patterns of space use of two Critically Endangered Galapagos tortoise species, Chelonoidis porteri and Chelonoidis donfaustoi, on privately owned and agricultural land (hereafter farms) on Santa Cruz Island, where a human–wildlife conflict is emerging. We used GPS data from 45 tortoises tracked for up to 9 years, and data on farm characteristics, to identify factors that influence tortoise movement and habitat use in the agricultural zone. Sixty-nine per cent of tagged tortoises used the agricultural zone, where they remained for a mean of 150 days before returning to the national park. Large male tortoises were more likely to use farms for longer periods than female and smaller individuals. Tortoises were philopatric (mean overlap of farmland visits = 88.7 ± SE 2.9%), on average visiting four farms and occupying a mean seasonal range of 2.9 ± SE 0.3 ha. We discuss the characteristics of farm use by tortoises, and its implications for tortoise conservation and coexistence with people.
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Nieto-Claudín A, Palmer JL, Esperón F, Deem SL. Haematology and plasma biochemistry reference intervals for the critically endangered western Santa Cruz Galapagos tortoise (C helonoidis porteri). CONSERVATION PHYSIOLOGY 2021; 9:coab019. [PMID: 33959287 PMCID: PMC8071477 DOI: 10.1093/conphys/coab019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 02/08/2021] [Accepted: 03/29/2021] [Indexed: 06/12/2023]
Abstract
Reference intervals (RIs) are an increasingly valuable tool for monitoring captive and free-living wildlife populations. Galapagos tortoises are one of the most emblematic species on Earth with 9 of the 12 extant species considered endangered due to human activities. As part of a long-term health assessment within the Galapagos Tortoise Movement Ecology Programme, we sampled a total of 210 free-living Santa Cruz Galapagos tortoises (Chelonoidis porteri). We collected blood from the brachial vein and performed packed cell volume (PCV), total solids (TS), morphological evaluation, white blood cell (WBC) count estimates and differentials and a VetScan biochemistry panel for each individual. We calculated 95% RIs and 90% confidence intervals (CIs) using the Reference Value Advisor tool and following international standard guidelines. Tortoises were categorized by estimated age and sex, with RI and CI reported here for 164 adult tortoises and 46 sub-adult tortoises. We found significant differences between sexes, with adult females presenting a lower PCV and higher values for both calcium and potassium. Among age groups, adult tortoises presented higher PCV, TS and albumin and lower WBC counts, aspartate aminotransferase and creatine kinase than sub-adult tortoises. We also found that tortoises presented higher numbers of lymphocytes during the dry season, but higher basophils, eosinophils, phosphorus, potassium and TS during the humid season. The heterophil:lymphocyte ratio did not differ between groups. To the authors' knowledge, this is the first report of formal plasma biochemistry and haematology RI for free-living Galapagos tortoises. With the present study we provide an important diagnostic tool for captive-breeding programs in the Galapagos and zoological institutions globally that care for giant tortoises. The ultimate goal of this study is to contribute to the understanding of giant tortoise baseline health parameters and to inform local management decisions that help to conserve these emblematic species.
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Affiliation(s)
- Ainoa Nieto-Claudín
- Charles Darwin Foundation, Charles Darwin Ave., Santa Cruz, 200350, Galapagos Islands, Ecuador
- Saint Louis Zoo Institute for Conservation Medicine, One Government Drive, Saint Louis, MO 63110, USA
- Complutense University of Madrid, Veterinary Faculty, Puerta de Hierro Ave, Madrid, 28040, Spain
| | - Jamie L Palmer
- Saint Louis Zoo Institute for Conservation Medicine, One Government Drive, Saint Louis, MO 63110, USA
| | - Fernando Esperón
- Complutense University of Madrid, Veterinary Faculty, Puerta de Hierro Ave, Madrid, 28040, Spain
- INIA-CISA, Algete-El Casar Road, Valdeolmos, 28130, Spain
| | - Sharon L Deem
- Charles Darwin Foundation, Charles Darwin Ave., Santa Cruz, 200350, Galapagos Islands, Ecuador
- Saint Louis Zoo Institute for Conservation Medicine, One Government Drive, Saint Louis, MO 63110, USA
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Ewbank AC, Esperón F, Sacristán C, Sacristán I, Neves E, Costa-Silva S, Antonelli M, Rocha Lorenço J, Kolesnikovas CKM, Catão-Dias JL. Occurrence and Quantification of Antimicrobial Resistance Genes in the Gastrointestinal Microbiome of Two Wild Seabird Species With Contrasting Behaviors. Front Vet Sci 2021; 8:651781. [PMID: 33829054 PMCID: PMC8019699 DOI: 10.3389/fvets.2021.651781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 02/24/2021] [Indexed: 01/24/2023] Open
Abstract
Antimicrobial resistance genes (ARGs) are environmental pollutants and anthropization indicators. We evaluated human interference in the marine ecosystem through the ocurrence and quantification (real-time PCRs) of 21 plasmid-mediated ARGs in enema samples of 25 wild seabirds, upon admission into rehabilitation: kelp gull (Larus dominicanus, n = 14) and Magellanic penguin (Spheniscus magellanicus, n = 11). Overall, higher resistance values were observed in kelp gulls (non-migratory coastal synanthropic) in comparison with Magellanic penguins (migratory pelagic non-synanthropic). There were significant differences between species (respectively, kelp gull and Magellanic penguin): ARGs occurrence (bla TEM [p = 0.032]; tetM [p = 0.015]; tetA [p = 0.003]; and sulII [p = 0.007]), mean number of ARGs per sample (p = 0.031), ARGs mean load percentage (aadA [p = 0.045], tetA [p = 0.031], tetM [p = 0.016], bla TEM [p = 0.032], sulII [p = 0.008]), percentage of genes conferring resistance to an antimicrobial class (betalactams [p = 0.036] and sulfonamides [p = 0.033]), mean number of genes conferring resistance to one or more antimicrobial classes (p = 0.024]), percentage of multiresistant microbiomes (p = 0.032), and clustering (p = 0.006). These differences are likely due to these species' contrasting biology and ecology - key factors in the epidemiology of ARGs in seabirds. Additionally, this is the first report of mecA in seabirds in the Americas. Further studies are necessary to clarify the occurrence and diversity of ARGs in seabirds, and their role as potential sources of infection and dispersal within the One Health chain of ARGs.
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Affiliation(s)
- Ana Carolina Ewbank
- Laboratory of Wildlife Comparative Pathology, Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Fernando Esperón
- Group of Epidemiology and Environmental Health, Animal Health Research Centre (INIA-CISA), Madrid, Spain
| | - Carlos Sacristán
- Laboratory of Wildlife Comparative Pathology, Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Irene Sacristán
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Elena Neves
- Group of Epidemiology and Environmental Health, Animal Health Research Centre (INIA-CISA), Madrid, Spain
| | | | | | | | | | - José Luiz Catão-Dias
- Laboratory of Wildlife Comparative Pathology, Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
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Ewbank AC, Esperón F, Sacristán C, Sacristán I, Krul R, Cavalcante de Macedo E, Calatayud O, Bueno I, de Francisco Strefezzi R, Catão-Dias JL. Seabirds as anthropization indicators in two different tropical biotopes: A One Health approach to the issue of antimicrobial resistance genes pollution in oceanic islands. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 754:142141. [PMID: 32920402 DOI: 10.1016/j.scitotenv.2020.142141] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/29/2020] [Accepted: 08/31/2020] [Indexed: 05/12/2023]
Abstract
Antimicrobial resistance is a quintessential One Health issue, among the most serious 21st century global threats to human health. Seabirds may act as sentinels of natural and anthropogenic changes in the marine ecosystem health, including pollution by antimicrobial resistance genes (ARGs). We used real time PCR to identify and quantify 22 plasmid-mediated ARGs in the gastrointestinal microbiome of six wild seabird species, comparing an anthropized (Fernando de Noronha Archipelago - FNA) and a pristine biotope (Rocas Atoll - ROA), Brazil. Of 257 birds, 218 (84.8%) were positive to at least one ARG. ARG classes encoding resistance to tetracyclines (75.1%), quinolones (10.5%) and phenicols (10.5%) were the most prevalent, with tetracyclines significantly greater than the remaining classes (p < 0.05). Genes tet(S) (29.2%), tet(A) (28.8%), and tet(B) (24.9%) were the most commonly found and had a significantly greater prevalence when compared to the remaining ARGs (p < 0.05). The anthropized biotope presented statistically significant higher prevalence of sulfonamide- and quinolone-encoding ARGs in comparison with the pristine (respectively, p = 0.01 and p = 0.03), and higher sulII gene prevalence (p = 0.04), consistent with anthropogenic pressure. Migratory species (only present in ROA) showed statistically significant higher mcr-1 (polymyxins) and blaTEM (betalactam) prevalences (respectively, p = 0.009 and p = 0.02), and mcr-1 percentage load (p = 0.0079) in comparison with non-migratory. To our knowledge, this is the largest ARGs survey based on direct detection and quantification in seabirds worldwide, and the first to evaluate non-synanthropic species in oceanic islands. This is the first detection of mcr-1 in wild free-ranging seabirds in Brazil and in free-ranging migratory non-synanthropic seabirds worldwide. Our findings show the importance of biological and ecological factors, highlighting the role of seabirds as anthropization sentinels and ARGs-pollution environmental indicators (even in a pristine biotope), and their involvement in the One Health epidemiological chain of ARGs.
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Affiliation(s)
- Ana Carolina Ewbank
- Laboratory of Wildlife Comparative Pathology, Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil.
| | - Fernando Esperón
- Group of Epidemiology and Environmental Health, Animal Health Research Centre (INIA-CISA), Madrid, Spain.
| | - Carlos Sacristán
- Laboratory of Wildlife Comparative Pathology, Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil.
| | - Irene Sacristán
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.
| | - Ricardo Krul
- Ornithology Laboratory, Center for Studies of the Sea, Paraná State University, Paraná State, Brazil.
| | - Eduardo Cavalcante de Macedo
- Chico Mendes Institute for Biodiversity Conservation (ICMBio) - Brazilian Ministry of the Environment, Rocas Atol Biological Reserve, Rio Grande do Norte, Brazil.
| | - Olga Calatayud
- Group of Epidemiology and Environmental Health, Animal Health Research Centre (INIA-CISA), Madrid, Spain.
| | - Irene Bueno
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, United States.
| | - Ricardo de Francisco Strefezzi
- Laboratory of Comparative and Translational Oncology, Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, Brazil.
| | - José Luiz Catão-Dias
- Laboratory of Wildlife Comparative Pathology, Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil.
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10
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Esperón F, Albero B, Ugarte-Ruíz M, Domínguez L, Carballo M, Tadeo JL, Del Mar Delgado M, Moreno MÁ, de la Torre A. Assessing the benefits of composting poultry manure in reducing antimicrobial residues, pathogenic bacteria, and antimicrobial resistance genes: a field-scale study. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:27738-27749. [PMID: 32399873 DOI: 10.1007/s11356-020-09097-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 04/28/2020] [Indexed: 06/11/2023]
Abstract
The poultry industry in the European Union produces 13 million tons of manure annually, which represents a major health and environmental challenge. Composting is an environmental-friendly technique for the management of manure, but there are few studies about antibiotic residues and antimicrobial resistances at a field scale. The goal of this study was to determine if the composting of poultry manure at a field scale would result in the reduction of antibiotic residues, pathogenic bacteria, and antibiotic resistance genes (ARGs) in the final fertilizer product. A 10-week composting of poultry manure spiked with enrofloxacin, doxycycline, and ciprofloxacin was performed. The determination of antibiotics residues and 22 selected ARGs was carried out together with the identification of bacteria by metagenomics. In the case of ciprofloxacin and doxycycline, a 90% decrease was observed after composting for 3 weeks. Sixteen ARGs were detected at the beginning of the experiment; 12 of them decreased from week 0 to week 10 (reduction of 73.7-99.99%). The presence of potentially pathogenic bacteria, such as, Campylobacter coli or commensal bacteria such as Escherichia coli decreases along the composting process. In conclusion, 10-week composting of poultry manure promotes the reduction of antibiotic residues and most of the ARGs and pathogenic bacteria.
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Affiliation(s)
- Fernando Esperón
- Animal Health Research Center (INIA-CISA), Ctra Algete a El Casar s/n, 28130, Valdeolmos, Madrid, Spain.
| | - Beatriz Albero
- Department of Environment and Agronomy (INIA), Ctra La Coruña Km. 7.5, 28040, Madrid, Spain
| | - María Ugarte-Ruíz
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Avda. Puerta de Hierro, s/n, 28040, Madrid, Spain
| | - Lucas Domínguez
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Avda. Puerta de Hierro, s/n, 28040, Madrid, Spain
- Department of Animal Health, Veterinary Faculty, Complutense University of Madrid, Ada. Puerta de Hierro, s/n, Madrid, Spain
| | - Matilde Carballo
- Animal Health Research Center (INIA-CISA), Ctra Algete a El Casar s/n, 28130, Valdeolmos, Madrid, Spain
| | - José Luis Tadeo
- Department of Environment and Agronomy (INIA), Ctra La Coruña Km. 7.5, 28040, Madrid, Spain
| | - María Del Mar Delgado
- Department of Environment and Agronomy (INIA), Ctra La Coruña Km. 7.5, 28040, Madrid, Spain
| | - Miguel Ángel Moreno
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Avda. Puerta de Hierro, s/n, 28040, Madrid, Spain
- Department of Animal Health, Veterinary Faculty, Complutense University of Madrid, Ada. Puerta de Hierro, s/n, Madrid, Spain
| | - Ana de la Torre
- Animal Health Research Center (INIA-CISA), Ctra Algete a El Casar s/n, 28130, Valdeolmos, Madrid, Spain
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11
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McKnight DT, Zenger KR, Alford RA, Huerlimann R. Microbiome diversity and composition varies across body areas in a freshwater turtle. MICROBIOLOGY-SGM 2020; 166:440-452. [PMID: 32213245 DOI: 10.1099/mic.0.000904] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
There is increasing recognition that microbiomes are important for host health and ecology, and understanding host microbiomes is important for planning appropriate conservation strategies. However, microbiome data are lacking for many taxa, including turtles. To further our understanding of the interactions between aquatic microbiomes and their hosts, we used next generation sequencing technology to examine the microbiomes of the Krefft's river turtle (Emydura macquarii krefftii). We examined the microbiomes of the buccal (oral) cavity, skin on the head, parts of the shell with macroalgae and parts of the shell without macroalgae. Bacteria in the phyla Proteobacteria and Bacteroidetes were the most common in most samples (particularly buccal samples), but Cyanobacteria, Deinococcus-thermus and Chloroflexi were also common (particularly in external microbiomes). We found significant differences in community composition among each body area, as well as significant differences among individuals. The buccal cavity had lower bacterial richness and evenness than any of the external microbiomes, and it had many amplicon sequence variants (ASVs) with a low relative abundance compared to other body areas. Nevertheless, the buccal cavity also had the most unique ASVs. Parts of the shell with and without algae also had different microbiomes, with particularly obvious differences in the relative abundances of the families Methylomonaceae, Saprospiraceae and Nostocaceae. This study provides novel, baseline information about the external microbiomes of turtles and is a first step in understanding their ecological roles.
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Affiliation(s)
- Donald T McKnight
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia.,Present address: School of Environmental and Rural Science, University of New England, Armidale, New South Wales, Australia
| | - Kyall R Zenger
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Ross A Alford
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Roger Huerlimann
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
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