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Freitas ADAR, Faria AR, Mendes LT, Merquior VLC, Neves DM, Pires JR, Teixeira LM. The gut microbiota of wild birds undergoing rehabilitation as a reservoir of multidrug-resistant enterococci in a metropolitan area in Brazil. Braz J Microbiol 2024:10.1007/s42770-024-01527-3. [PMID: 39356407 DOI: 10.1007/s42770-024-01527-3] [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: 05/29/2024] [Accepted: 09/14/2024] [Indexed: 10/03/2024] Open
Abstract
Enterococci are ubiquitous usually commensal bacteria that can act as opportunistic pathogens frequently associated with resistance to multiple antimicrobial classes. A variety of animals may carry potentially harmful enterococci. In the present work, the occurrence and characteristics of enterococci recovered from the fecal microbiota of wild birds belonging to four families (Accipitridae, Cathartidae, Falconidae and Strigidae) were investigated. Enterococci were recovered from 104 (92.0%) fecal samples obtained from 113 birds, and 260 strains were selected for additional characterization. Enterococcus faecalis was the predominant species (63.8%), followed by Enterococcus hirae (16.2%), Enterococcus faecium (11.5%), Enterococcus gallinarum (5.4%), Enterococcus avium (1.5%), Enterococcus casseliflavus (0.8%), and Enterococcus raffinosus and Enterococcus cecorum (0.4% each). Major percentages (11.9% 75.0%) of nonsusceptibility were observed to quinolones (particularly to enrofloxacin), erythromycin, rifampin, nitrofurantoin, tetracycline and streptomycin. Gentamicin and ampicillin resistances (13.3% each) were only detected among E. faecium. A total of 133 (51.2%) strains were MDR, showing a large variety of MDR profiles, composed by simultaneous resistance encompassing 3 to 12 antimicrobials. MDR strains were found in 68.2% of the birds. Antimicrobial resistance was associated with the presence of the aac(6')-aph(2″)-Ia, aph(2″)-Id, ant(6)-Ia, ant(9)-Ia, ant(9)-Ib, tet(M), tet(L), tet(S), erm(B), mef(A/E), msrC, and vat(D) genes. The most common virulence genes were efaA, gelE, ace, eeP, and asa1. PFGE analysis revealed a large genetic diversity among most of the strains. MLST performed for 35 E. faecalis strains revealed 23 different STs, whereas 14 STs were found among 18 E. faecium strains. Hospital-associated lineages ST22, ST25, ST56, ST1274 were identified. The results show that the wild birds investigated can carry a diversity of potentially hazardous enterococcal strains displaying multiple antimicrobial resistance and virulence genes, reinforcing the assumption that these animals provide an important target to monitor the circulation of microorganisms that deserve consideration under the One Health perspective.
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Affiliation(s)
| | - Adriana Rocha Faria
- Instituto de Microbiologia Paulo de Góes, Universidade Federal Do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
- Departamento de Microbiologia, Imunologia E Parasitologia, Universidade Do Estado Do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
- Faculdade de Medicina, Universidade Federal Do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Luiza Tomé Mendes
- Instituto de Microbiologia Paulo de Góes, Universidade Federal Do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Vânia Lúcia Carreira Merquior
- Departamento de Microbiologia, Imunologia E Parasitologia, Universidade Do Estado Do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Daniel Marchesi Neves
- Centro de Triagem de Animais, Silvestres Do Rio de Janeiro (CETAS-RJ), Seropédica, RJ, Brazil
| | - Jeferson Rocha Pires
- Centro de Reabilitação de Animais Selvagens da Universidade Estácio de Sá (CRAS-UNESA), Rio de Janeiro, RJ, Brazil
| | - Lúcia Martins Teixeira
- Instituto de Microbiologia Paulo de Góes, Universidade Federal Do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
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Mocellin RR, Toigo AL, Dos Santos CC, Frazzon J, Nunes GT, Bugoni L, Prichula J, Frazzon APG. Metal tolerance in enterococci isolated from seabirds in Abrolhos Archipelago, Brazil: Evaluating their role as bioindicators of marine pollution. MARINE POLLUTION BULLETIN 2024; 207:116866. [PMID: 39216259 DOI: 10.1016/j.marpolbul.2024.116866] [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: 05/16/2024] [Revised: 08/06/2024] [Accepted: 08/15/2024] [Indexed: 09/04/2024]
Abstract
Microbiota exposed to pollution provide insights into host physiology and ecosystem disruption. This study evaluated Enterococcus spp. tolerant to arsenic (As), copper (Cu), and mercury (Hg) from red-billed tropicbirds (Phaethon aethereus) and brown boobies (Sula leucogaster), which previously showed these metals in their blood and feathers, and their potential use as bioindicators of metal contamination. Enterococcus casseliflavus (47.9 %), E. faecalis (34.1 %), E. hirae (11.7 %), and E. faecium (5.3 %) were identified. Both seabird species had a high incidence of As-tolerant bacteria (84.0 %), with 40.4 % of these strains containing As efflux system genes (arsA_I and arsA_II). Cu efflux pump gene (tcrB) was detected in 30.9 % of strains, while Hg reductase genes (mer) were not found. As- and Cu-tolerance in enterococci observed in this study underlines their potential as bioindicators in metal-polluted marine environments. Further research may elucidate the role of these metal-tolerant enterococci in seabird gut and their adaptability to polluted environments.
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Affiliation(s)
- Raquel Rita Mocellin
- Programa de Pós-Graduação em Microbiologia Agrícola e do Ambiente, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul - UFRGS, Rua Ramiro Barcelos, 2600, 90035-003 Porto Alegre, RS, Brazil
| | - Amanda Ladeira Toigo
- Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul - UFRGS, Rua Ramiro Barcelos, 2600, 90035-003 Porto Alegre, RS, Brazil
| | - Camila Coutinho Dos Santos
- Programa de Pós-Graduação em Microbiologia Agrícola e do Ambiente, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul - UFRGS, Rua Ramiro Barcelos, 2600, 90035-003 Porto Alegre, RS, Brazil
| | - Jeverson Frazzon
- Departamento de Ciência de Alimentos, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul - UFRGS, Av. Bento Gonçalves, 9500, 91501-970 Porto Alegre, RS, Brazil
| | - Guilherme Tavares Nunes
- Centro de Estudos Costeiros, Limnológicos e Marinhos, Universidade Federal do Rio Grande do Sul - UFRGS, Avenida Tramandaí, 976, 95625-000 Imbé, RS, Brazil
| | - Leandro Bugoni
- Laboratório de Aves Aquáticas e Tartarugas Marinhas, Universidade Federal do Rio Grande - FURG, Av. Itália, s/n, 96203-900 Rio Grande, RS, Brazil
| | - Janira Prichula
- Department of Ophthalmology, Mass Eye and Ear, Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Ana Paula Guedes Frazzon
- Programa de Pós-Graduação em Microbiologia Agrícola e do Ambiente, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul - UFRGS, Rua Ramiro Barcelos, 2600, 90035-003 Porto Alegre, RS, Brazil; Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul - UFRGS, Rua Ramiro Barcelos, 2600, 90035-003 Porto Alegre, RS, Brazil.
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3
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Loncaric I, Szostak MP, Cabal-Rosel A, Grünzweil OM, Riegelnegg A, Misic D, Müller E, Feßler AT, Braun SD, Schwarz S, Monecke S, Ehricht R, Ruppitsch W, Spergser J, Lewis A, Bloom PH, Saggese MD. Molecular characterization, virulence and antimicrobial and biocidal susceptibility of selected bacteria isolated from the cloaca of nestling ospreys (Pandion haliaetus) from Mono Lake, California, USA. PLoS One 2024; 19:e0311306. [PMID: 39331631 PMCID: PMC11432900 DOI: 10.1371/journal.pone.0311306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Accepted: 09/06/2024] [Indexed: 09/29/2024] Open
Abstract
In the present study, the presence of the Enterobacterales, Staphylococcus spp., Mammaliicoccus spp., and Enterococcus spp. in cloacal samples of nestling ospreys (Pandion haliaetus), a fish-eating specialist, from Mono Lake, California, USA was examined by a multiphasic approach, including antimicrobial and biocide susceptibility testing, genotyping, and whole genome sequencing of selected isolates. The most commonly detected species was Escherichia coli, followed by Mammaliicoccus sciuri, Staphylococcus delphini, Enterococcus faecalis, Enterococcus faecium, Hafnia alvei, Klebsiella pneumoniae, Citrobacter braakii and single isolates of Edwardsiella tarda, Edwardsiella albertii, Klebsiella aerogenes, Plesiomonas shigelloides and Staphylococcus pseudintermedius. Multi-drug resistance (MDR) was observed in two E. coli isolates and in an Enterococcus faecium isolate. The MDR blaCTX-M-55-positive E. coli belonged to the pandemic clone ST58. The results of the present study suggest that nestling ospreys are exposed to MDR bacteria, possibly through the ingestion of contaminated fish. Ospreys may be good biosentinels for the presence of these microorganisms and antibiotic resistance in the local environment and the risk for other wildlife, livestock and humans.
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Affiliation(s)
- Igor Loncaric
- Institute of Microbiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Michael P Szostak
- Institute of Microbiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Adriana Cabal-Rosel
- Austrian Agency for Health and Food Safety (AGES), Institute of Medical Microbiology and Hygiene, Vienna, Austria
| | - Olivia M Grünzweil
- Institute of Microbiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Alina Riegelnegg
- Institute of Microbiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Dusan Misic
- Department of Functional Food Products Development, Faculty of Biotechnology and Food Science, Wroclaw University of Environmental and Life Sciences, Wroclaw, Poland
| | - Elke Müller
- Leibniz Institute of Photonic Technology (IPHT), Jena, Germany
- InfectoGnostics Research Campus, Jena, Germany
| | - Andrea T Feßler
- Centre of Infection Medicine, School of Veterinary Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Sascha D Braun
- Leibniz Institute of Photonic Technology (IPHT), Jena, Germany
- InfectoGnostics Research Campus, Jena, Germany
| | - Stefan Schwarz
- Centre of Infection Medicine, School of Veterinary Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Stefan Monecke
- Leibniz Institute of Photonic Technology (IPHT), Jena, Germany
- InfectoGnostics Research Campus, Jena, Germany
- Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinik Dresden, Dresden, Germany
| | - Ralf Ehricht
- Leibniz Institute of Photonic Technology (IPHT), Jena, Germany
- InfectoGnostics Research Campus, Jena, Germany
- Institute of Physical Chemistry, Friedrich Schiller University, Jena, Germany
| | - Werner Ruppitsch
- Austrian Agency for Health and Food Safety (AGES), Institute of Medical Microbiology and Hygiene, Vienna, Austria
| | - Joachim Spergser
- Institute of Microbiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Ashli Lewis
- California State Parks, Grass Valley, CA, United States of America
| | - Peter H Bloom
- Bloom Research Inc, Santa Ana, CA, United States of America
| | - Miguel D Saggese
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA, United States of America
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Schwartzman JA, Lebreton F, Salamzade R, Shea T, Martin MJ, Schaufler K, Urhan A, Abeel T, Camargo ILBC, Sgardioli BF, Prichula J, Guedes Frazzon AP, Giribet G, Van Tyne D, Treinish G, Innis CJ, Wagenaar JA, Whipple RM, Manson AL, Earl AM, Gilmore MS. Global diversity of enterococci and description of 18 previously unknown species. Proc Natl Acad Sci U S A 2024; 121:e2310852121. [PMID: 38416678 DOI: 10.1073/pnas.2310852121] [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: 07/10/2023] [Accepted: 12/06/2023] [Indexed: 03/01/2024] Open
Abstract
Enterococci are gut microbes of most land animals. Likely appearing first in the guts of arthropods as they moved onto land, they diversified over hundreds of millions of years adapting to evolving hosts and host diets. Over 60 enterococcal species are now known. Two species, Enterococcus faecalis and Enterococcus faecium, are common constituents of the human microbiome. They are also now leading causes of multidrug-resistant hospital-associated infection. The basis for host association of enterococcal species is unknown. To begin identifying traits that drive host association, we collected 886 enterococcal strains from widely diverse hosts, ecologies, and geographies. This identified 18 previously undescribed species expanding genus diversity by >25%. These species harbor diverse genes including toxins and systems for detoxification and resource acquisition. Enterococcus faecalis and E. faecium were isolated from diverse hosts highlighting their generalist properties. Most other species showed a more restricted distribution indicative of specialized host association. The expanded species diversity permitted the Enterococcus genus phylogeny to be viewed with unprecedented resolution, allowing features to be identified that distinguish its four deeply rooted clades, and the entry of genes associated with range expansion such as B-vitamin biosynthesis and flagellar motility to be mapped to the phylogeny. This work provides an unprecedentedly broad and deep view of the genus Enterococcus, including insights into its evolution, potential new threats to human health, and where substantial additional enterococcal diversity is likely to be found.
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Affiliation(s)
- Julia A Schwartzman
- Department of Ophthalmology, Mass Eye and Ear, Harvard Medical School, Boston, MA 02144
- Department of Microbiology, Harvard Medical School, Boston, MA 02115
- Department of Biology, University of Southern California, Los Angeles, CA 90089
| | - Francois Lebreton
- Department of Ophthalmology, Mass Eye and Ear, Harvard Medical School, Boston, MA 02144
- Department of Microbiology, Harvard Medical School, Boston, MA 02115
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD 20910
| | - Rauf Salamzade
- Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706
| | - Terrance Shea
- Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142
| | - Melissa J Martin
- Department of Ophthalmology, Mass Eye and Ear, Harvard Medical School, Boston, MA 02144
- Department of Microbiology, Harvard Medical School, Boston, MA 02115
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD 20910
| | - Katharina Schaufler
- Department of Ophthalmology, Mass Eye and Ear, Harvard Medical School, Boston, MA 02144
- Department of Microbiology, Harvard Medical School, Boston, MA 02115
- University of Greifswald, Institute of Pharmacy, Greifswald 17489, Germany
- Kiel University and University Medical Center Schleswig-Holstein, Institute of Infection Medicine, Kiel 24105, Germany
| | - Aysun Urhan
- Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142
- Delft Bioinformatics Lab, Department of Intelligent Systems, Delft University of Technology, Delft 2628XE, The Netherlands
| | - Thomas Abeel
- Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142
- Delft Bioinformatics Lab, Department of Intelligent Systems, Delft University of Technology, Delft 2628XE, The Netherlands
| | - Ilana L B C Camargo
- Laboratório de Epidemiologia e Microbiologia Moleculares, Departamento de Física e Ciências Interdisciplinares, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos - SP 13566-590, Brazil
| | - Bruna F Sgardioli
- Laboratório de Epidemiologia e Microbiologia Moleculares, Departamento de Física e Ciências Interdisciplinares, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos - SP 13566-590, Brazil
| | - Janira Prichula
- Department of Ophthalmology, Mass Eye and Ear, Harvard Medical School, Boston, MA 02144
- Department of Microbiology, Harvard Medical School, Boston, MA 02115
- Federal University of Health Sciences of Porto Alegre, Porto Alegre - RS 90050-170, Brazil
| | - Ana Paula Guedes Frazzon
- Department of Ophthalmology, Mass Eye and Ear, Harvard Medical School, Boston, MA 02144
- Department of Microbiology, Harvard Medical School, Boston, MA 02115
- Department of Microbiology, Immunology and Parasitology, Federal University of Rio Grande do Sul, Porto Alegre - RS, 90010-150, Brazil
| | - Gonzalo Giribet
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138
| | - Daria Van Tyne
- Department of Ophthalmology, Mass Eye and Ear, Harvard Medical School, Boston, MA 02144
- Department of Microbiology, Harvard Medical School, Boston, MA 02115
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburg, PA 15213
| | | | - Charles J Innis
- New England Aquarium, Animal Health Department and Anderson Cabot Center for Ocean Life, Boston, MA 02110
| | - Jaap A Wagenaar
- Department of Biomolecular Health Sciences, Utrecht University, Utrecht 3584 CS, The Netherlands
| | - Ryan M Whipple
- Department of Ophthalmology, Mass Eye and Ear, Harvard Medical School, Boston, MA 02144
- Department of Microbiology, Harvard Medical School, Boston, MA 02115
| | - Abigail L Manson
- Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142
| | - Ashlee M Earl
- Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142
| | - Michael S Gilmore
- Department of Ophthalmology, Mass Eye and Ear, Harvard Medical School, Boston, MA 02144
- Department of Microbiology, Harvard Medical School, Boston, MA 02115
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Harris S, Scioscia G, Raya Rey A. The influence of tourist visitation on the heterophyl to lymphocyte ratios and trophic values of Magellanic penguins ( Spheniscus magellanicus) at Martillo Island, Argentina. CONSERVATION PHYSIOLOGY 2023; 11:coad063. [PMID: 38053739 PMCID: PMC10694407 DOI: 10.1093/conphys/coad063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 07/18/2023] [Accepted: 08/14/2023] [Indexed: 12/07/2023]
Abstract
Wildlife tourism is increasing worldwide and monitoring the impact of tourism on wild populations is of the utmost importance for species conservation. The Magellanic penguin Spheniscus magellanicus colony at Martillo Island, Argentina, was studied in the 2016-2020 breeding seasons. In all seasons, adults and chicks belonged to: (i) an area close to or within the tourist trail or (ii) an area far from the tourist trail and out of sight of the tourists. Blood samples were taken for carbon and nitrogen stable isotope composition, in order to estimate trophic niches, and for smears that were made in situ and were then stained in the laboratory where leucocyte counts and differentiation were made under optical microscope. Heterophil to lymphocyte ratios were used as proxies of stress. Repeated sampling showed individual stress levels reduced while wintering. In 2017, stress levels and trophic values were lower than 2018 for the same individuals. Trophic levels did not differ between tourism and no tourism areas within each season, and differed between 2017 and the remaining seasons, indicating a possible diet shift that year. Stress levels were higher for the tourism area than the no tourism area for adults and chicks in all years except for 2020, when stress levels in the tourism area were lower and similar to the no tourism area that year and previous years. Vessel transit within the Beagle Channel and tourist visitation to the penguin colony was greatly reduced in 2020 due to the Covid-19 pandemic. A combination of internal characteristics and external factors may be affecting the stress physiology of individuals. Therefore, future research should include sampling of multiple aspects of penguin physiology, behaviour and environmental context in order to evaluate each effect on Magellanic penguin stress and, ultimately, inform the conservation of this iconic species in time.
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Affiliation(s)
- Sabrina Harris
- Laboratorio de Ecología y Conservación de Vida silvestre, Centro Austral de Investigaciones Científicas, Consejo Nacional de Investigaciones Científicas y Técnicas, Houssay 200 (9410) Ushuaia, Tierra del Fuego, Argentina
- Wildlife Conservation Society representación Argentina, Amenábar 1595 piso 2 oficina 19 (1426) CABA, Buenos Aires, Argentina
| | - Gabriela Scioscia
- Laboratorio de Ecología y Conservación de Vida silvestre, Centro Austral de Investigaciones Científicas, Consejo Nacional de Investigaciones Científicas y Técnicas, Houssay 200 (9410) Ushuaia, Tierra del Fuego, Argentina
| | - Andrea Raya Rey
- Laboratorio de Ecología y Conservación de Vida silvestre, Centro Austral de Investigaciones Científicas, Consejo Nacional de Investigaciones Científicas y Técnicas, Houssay 200 (9410) Ushuaia, Tierra del Fuego, Argentina
- Wildlife Conservation Society representación Argentina, Amenábar 1595 piso 2 oficina 19 (1426) CABA, Buenos Aires, Argentina
- Instituto de Ciencias Polares, Ambiente y Recursos Naturales (ICPA), Universidad de Tierra del Fuego (UNTDF), Walanika 250 (9410) Ushuaia, Tierra del Fuego, Argentina
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Monteiro Marques J, Coelho M, Santana AR, Pinto D, Semedo-Lemsaddek T. Dissemination of Enterococcal Genetic Lineages: A One Health Perspective. Antibiotics (Basel) 2023; 12:1140. [PMID: 37508236 PMCID: PMC10376465 DOI: 10.3390/antibiotics12071140] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/22/2023] [Accepted: 06/29/2023] [Indexed: 07/30/2023] Open
Abstract
Enterococcus spp. are commensals of the gastrointestinal tracts of humans and animals and colonize a variety of niches such as water, soil, and food. Over the last three decades, enterococci have evolved as opportunistic pathogens, being considered ESKAPE pathogens responsible for hospital-associated infections. Enterococci's ubiquitous nature, excellent adaptative capacity, and ability to acquire virulence and resistance genes make them excellent sentinel proxies for assessing the presence/spread of pathogenic and virulent clones and hazardous determinants across settings of the human-animal-environment triad, allowing for a more comprehensive analysis of the One Health continuum. This review provides an overview of enterococcal fitness and pathogenic traits; the most common clonal complexes identified in clinical, veterinary, food, and environmental sources; as well as the dissemination of pathogenic genomic traits (virulome, resistome, and mobilome) found in high-risk clones worldwide, across the One Health continuum.
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Affiliation(s)
- Joana Monteiro Marques
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Av. da Universidade Técnica de Lisboa, 1300-477 Lisbon, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisbon, Portugal
| | - Mariana Coelho
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Av. da Universidade Técnica de Lisboa, 1300-477 Lisbon, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisbon, Portugal
| | - Andressa Rodrigues Santana
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Av. da Universidade Técnica de Lisboa, 1300-477 Lisbon, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisbon, Portugal
| | - Daniel Pinto
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Av. da Universidade Técnica de Lisboa, 1300-477 Lisbon, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisbon, Portugal
| | - Teresa Semedo-Lemsaddek
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Av. da Universidade Técnica de Lisboa, 1300-477 Lisbon, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisbon, Portugal
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7
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Prichula J, Primon-Barros M, Luz RCZ, Castro ÍMS, Paim TGS, Tavares M, Ligabue-Braun R, d’Azevedo PA, Frazzon J, Frazzon APG, Seixas A, Gilmore MS. Genome Mining for Antimicrobial Compounds in Wild Marine Animals-Associated Enterococci. Mar Drugs 2021; 19:328. [PMID: 34204046 PMCID: PMC8229437 DOI: 10.3390/md19060328] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 05/28/2021] [Accepted: 06/03/2021] [Indexed: 12/20/2022] Open
Abstract
New ecosystems are being actively mined for new bioactive compounds. Because of the large amount of unexplored biodiversity, bacteria from marine environments are especially promising. Further, host-associated microbes are of special interest because of their low toxicity and compatibility with host health. Here, we identified and characterized biosynthetic gene clusters encoding antimicrobial compounds in host-associated enterococci recovered from fecal samples of wild marine animals remote from human-affected ecosystems. Putative biosynthetic gene clusters in the genomes of 22 Enterococcus strains of marine origin were predicted using antiSMASH5 and Bagel4 bioinformatic software. At least one gene cluster encoding a putative bioactive compound precursor was identified in each genome. Collectively, 73 putative antimicrobial compounds were identified, including 61 bacteriocins (83.56%), 10 terpenes (13.70%), and 2 (2.74%) related to putative nonribosomal peptides (NRPs). Two of the species studied, Enterococcus avium and Enterococcus mundtti, are rare causes of human disease and were found to lack any known pathogenic determinants but yet possessed bacteriocin biosynthetic genes, suggesting possible additional utility as probiotics. Wild marine animal-associated enterococci from human-remote ecosystems provide a potentially rich source for new antimicrobial compounds of therapeutic and industrial value and potential probiotic application.
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Affiliation(s)
- Janira Prichula
- Gram-Positive Cocci Laboratory, Federal University of Health Sciences of Porto Alegre (UFCSPA), Porto Alegre 90050-170, RS, Brazil; (J.P.); (M.P.-B.); (R.C.Z.L.); (Í.M.S.C.); (T.G.S.P.); (P.A.d.)
| | - Muriel Primon-Barros
- Gram-Positive Cocci Laboratory, Federal University of Health Sciences of Porto Alegre (UFCSPA), Porto Alegre 90050-170, RS, Brazil; (J.P.); (M.P.-B.); (R.C.Z.L.); (Í.M.S.C.); (T.G.S.P.); (P.A.d.)
| | - Romeu C. Z. Luz
- Gram-Positive Cocci Laboratory, Federal University of Health Sciences of Porto Alegre (UFCSPA), Porto Alegre 90050-170, RS, Brazil; (J.P.); (M.P.-B.); (R.C.Z.L.); (Í.M.S.C.); (T.G.S.P.); (P.A.d.)
| | - Ícaro M. S. Castro
- Gram-Positive Cocci Laboratory, Federal University of Health Sciences of Porto Alegre (UFCSPA), Porto Alegre 90050-170, RS, Brazil; (J.P.); (M.P.-B.); (R.C.Z.L.); (Í.M.S.C.); (T.G.S.P.); (P.A.d.)
| | - Thiago G. S. Paim
- Gram-Positive Cocci Laboratory, Federal University of Health Sciences of Porto Alegre (UFCSPA), Porto Alegre 90050-170, RS, Brazil; (J.P.); (M.P.-B.); (R.C.Z.L.); (Í.M.S.C.); (T.G.S.P.); (P.A.d.)
| | - Maurício Tavares
- Centro de Estudos Costeiros, Limnológicos e Marinhos (CECLIMAR), Universidade Federal do Rio Grande do Sul (UFRGS), Campus Litoral Norte, Imbé 95625-000, RS, Brazil;
| | - Rodrigo Ligabue-Braun
- Department of Pharmacosciences, UFCSPA, Porto Alegre 90050-170, RS, Brazil; (R.L.-B.); (A.S.)
| | - Pedro A. d’Azevedo
- Gram-Positive Cocci Laboratory, Federal University of Health Sciences of Porto Alegre (UFCSPA), Porto Alegre 90050-170, RS, Brazil; (J.P.); (M.P.-B.); (R.C.Z.L.); (Í.M.S.C.); (T.G.S.P.); (P.A.d.)
| | - Jeverson Frazzon
- Food Science Institute, UFRGS, Porto Alegre 90035-003, RS, Brazil;
| | - Ana P. G. Frazzon
- Department of Microbiology, Immunology and Parasitology, UFRGS, Porto Alegre 90050-170, RS, Brazil;
| | - Adriana Seixas
- Department of Pharmacosciences, UFCSPA, Porto Alegre 90050-170, RS, Brazil; (R.L.-B.); (A.S.)
| | - Michael S. Gilmore
- Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
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8
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Pöntinen AK, Top J, Arredondo-Alonso S, Tonkin-Hill G, Freitas AR, Novais C, Gladstone RA, Pesonen M, Meneses R, Pesonen H, Lees JA, Jamrozy D, Bentley SD, Lanza VF, Torres C, Peixe L, Coque TM, Parkhill J, Schürch AC, Willems RJL, Corander J. Apparent nosocomial adaptation of Enterococcus faecalis predates the modern hospital era. Nat Commun 2021; 12:1523. [PMID: 33750782 PMCID: PMC7943827 DOI: 10.1038/s41467-021-21749-5] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 02/05/2021] [Indexed: 12/20/2022] Open
Abstract
Enterococcus faecalis is a commensal and nosocomial pathogen, which is also ubiquitous in animals and insects, representing a classical generalist microorganism. Here, we study E. faecalis isolates ranging from the pre-antibiotic era in 1936 up to 2018, covering a large set of host species including wild birds, mammals, healthy humans, and hospitalised patients. We sequence the bacterial genomes using short- and long-read techniques, and identify multiple extant hospital-associated lineages, with last common ancestors dating back as far as the 19th century. We find a population cohesively connected through homologous recombination, a metabolic flexibility despite a small genome size, and a stable large core genome. Our findings indicate that the apparent hospital adaptations found in hospital-associated E. faecalis lineages likely predate the "modern hospital" era, suggesting selection in another niche, and underlining the generalist nature of this nosocomial pathogen.
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Affiliation(s)
- Anna K Pöntinen
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway.
| | - Janetta Top
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Sergio Arredondo-Alonso
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Ana R Freitas
- UCIBIO/REQUIMTE, Laboratory of Microbiology, Biological Sciences Department, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Carla Novais
- UCIBIO/REQUIMTE, Laboratory of Microbiology, Biological Sciences Department, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Rebecca A Gladstone
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Maiju Pesonen
- Oslo Centre for Biostatistics and Epidemiology (OCBE), Oslo University Hospital Research Support Services, Oslo, Norway
| | - Rodrigo Meneses
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Henri Pesonen
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - John A Lees
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Dorota Jamrozy
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
| | | | | | - Carmen Torres
- Department of Food and Agriculture, Area of Biochemistry and Molecular Biology, University of La Rioja, Logroño, Spain
| | - Luisa Peixe
- UCIBIO/REQUIMTE, Laboratory of Microbiology, Biological Sciences Department, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Teresa M Coque
- Department of Microbiology, Ramón y Cajal Institute for Health Research Ramón y Cajal University Hospital, Madrid, Spain
- CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Julian Parkhill
- Wellcome Sanger Institute, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Anita C Schürch
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rob J L Willems
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jukka Corander
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway.
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK.
- Helsinki Institute of Information Technology, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland.
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