27 results on '"Prichula J"'
Search Results
2. The oral bacterial community in melanophryniscus admirabilis (Admirable red-belly toads): Implications for conservation
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Mann, M, Prichula, J, de Castro, I, Severo, J, Abadie, M, Lima, T, Caorsi, V, Borges-Martins, M, Frazzon, J, Frazzon, A, Mann M. B., Prichula J., de Castro I. M. S., Severo J. M., Abadie M., Lima T. M. D. F., Caorsi V., Borges-Martins M., Frazzon J., Frazzon A. P. G., Mann, M, Prichula, J, de Castro, I, Severo, J, Abadie, M, Lima, T, Caorsi, V, Borges-Martins, M, Frazzon, J, Frazzon, A, Mann M. B., Prichula J., de Castro I. M. S., Severo J. M., Abadie M., Lima T. M. D. F., Caorsi V., Borges-Martins M., Frazzon J., and Frazzon A. P. G.
- Abstract
Melanophryniscus admirabilis (admirable red-belly toad) is a microendemic and critically endangered species found exclusively along 700 m of the Forqueta River, in a fragment of the Atlantic Forest of southern Brazil. One of the greatest concerns regarding the conservation of this species is the extensive use of pesticides in areas surrounding their natural habitat. In recent years, the adaptation and persistence of animal species in human-impacted environments have been associated with microbiota. Therefore, the present study aimed to characterize the oral bacterial community of wild M. admirabilis and to address the question of how this community might contribute to this toad’s adaptation in the anthropogenic environment as well as its general metabolic capabilities. A total of 11 oral samples collected from wild M. admirabilis were characterized and analyzed via high-throughput sequencing. Fragments of the 16S rRNA variable region 4 (V4) were amplified, and sequencing was conducted using an Ion Personal Genome Machine (PGM) System with 316 chips. A total of 181,350 sequences were obtained, resulting in 16 phyla, 34 classes, 39 orders, and 77 families. Proteobacteria dominated (53%) the oral microbiota of toads, followed by Firmicutes (18%), Bac-teroidetes (17%), and Actinobacteria (5%). No significant differences in microbial community profile from among the samples were reported, which suggests that the low dietary diversity observed in this population may directly influence the bacterial composition. Inferences of microbiome function were performed using PICRUSt2 software. Important pathways (e.g., xenobiotic degradation pathways for pesticides and aromatic phenolic compounds) were detected, which suggests that the bacterial communities may serve important roles in M. admirabilis health and survival in the anthropogenic environment. Overall, our results have important implications for the conservation and management of this microendemic and critically endangere
- Published
- 2021
3. Frequency of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) in non-clinical Enterococcus faecalis and Enterococcus faecium strains
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Huescas, C. G. Y., Pereira, R. I., Prichula, J., Azevedo, P. A., Frazzon, J., and Frazzon, A. P. G.
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CRISPRs ,amostras fecais ,food samples ,fecal samples ,amostras alimentares ,animais marinhos selvagens ,Enterococcus faecium ,Enterococcus faecalis ,wild marine animals - Abstract
The fidelity of the genomes is defended by mechanism known as Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) systems. Three Type II CRISPR systems (CRISPR1- cas, CRISPR2 and CRISPR3-cas) have been identified in enterococci isolates from clinical and environmental samples. The aim of this study was to observe the distribution of CRISPR1-cas, CRISPR2 and CRISPR3-cas in non-clinical strains of Enterococcus faecalis and Enterococcus faecium isolates from food and fecal samples, including wild marine animals. The presence of CRISPRs was evaluated by PCR in 120 enterococci strains, 67 E. faecalis and 53 E. faecium. It is the first report of the presence of the CRISPRs system in E. faecalis and E. faecium strains isolated from wild marine animal fecal samples. The results showed that in non-clinical strains, the CRISPRs were more frequently detected in E. faecalis than in E. faecium. And the frequencies of CRISPR1-cas and CRISPR2 were higher (60%) in E. faecalis strains isolated from animal feces, compared to food samples. Both strains showed low frequencies of CRISPR3-cas (8.95% and 1.88%). In conclusion, the differences in the habitats of enterococcal species may be related with the results observe in distribution of CRISPRs systems. Resumo A fidelidade dos genomas é defendida por mecanismos conhecidos como sistemas de repetições palindrômicas curtas agrupadas e regularmente interespaçadas (CRISPRs). Três tipos de sistemas CRISPR II (CRISPR1-cas, CRISPR2 e CRISPR3-cas) têm sido identificados em cepas de enterococos isolados de amostras clínicas e ambientais. O objetivo deste estudo foi observar a distribuição dos CRISPR1-cas, CRISPR2 e CRISPR3-cas em cepas não-clínicas de Enterococcus faecalis e Enterococcus faecium isoladas de amostras alimentícias e fecais, incluindo animais marinhos selvagens. A presenca dos CRISPRs foi determinada por PCR em 120 cepas de enterococos, sendo 67 E. faecalis e 53 E. faecium. É o primeiro relato da presença do sistema CRISPRs nas estirpes E. faecalis e E. faecium isoladas de amostras fecais de animais marinhos selvagens. Os resultados mostraram que em cepas não-clínicas, os CRISPRs foram mais frequentemente detectados em E. faecalis do que em E. faecium. E as frequências de CRISPR1-cas e CRISPR2 foram maiores (60%) em cepas de E. faecalis isoladas de fezes de animais, quando comparadas à amostras de alimentos. Ambas as cepas apresentaram baixas freqüências de CRISPR3-cas (8,95% e 1,88%). Em conclusão, as diferenças nos habitats das espécies de enterococos podem estar relacionadas com os resultados observados na distribuição dos sistemas CRISPRs.
- Published
- 2018
4. LPDE biodegradation promoted by a novel additive based on silica nanoparticles: structural, microbial and ecotoxicological characterization.
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Miranda GM, Pivato AF, de Fraga FS, Machado VP, Lovato BP, Fricks AT, Santarém E, Prichula J, Trentin DS, de Lima JEA, and Ligabue RA
- Abstract
This study developed a biodegrading additive based on nanosilica and modified by cellulase enzyme in the presence of citric acid and sodium citrate. The additive was tested as a facilitator for biodegradation of the commercial low-density polyethylene (LDPE) in soil. Enzyme immobilization was confirmed by enzymatic assays. Moreover, additive and nanocomposites were characterized by spectroscopic and microscopic techniques. To assess the role of additive in biodegradation, CO
2 production in soil was measured at 30°C for 83 days. Biodegraded nanocomposites were cultivated to isolate possible LDPE-biodegrading microorganisms. Ecotoxicity of the studied materials was evaluated on cucumber (Cucumis sativus L.). CO2 production from LDPE/additive sample was similar to the starch (1055 ± 14 mg and 1078 ± 28 mg, respectively), and higher than pure LDPE (882 ± 34 mg) and LDPE/nanosilica (992 ± 30 mg). Although the presence of LDPE/nanosilica and LDPE/additive led to root length reduction of 24.3 ± 2.3% compared to the control (soil), the accumulation of root biomass was not affected. Furthermore, the nanocomposites did not cause harmful effects on seedling growth. Nine microbial isolates were recovered from biodegraded samples and identified by molecular techniques. It was demonstrated for the first time the LDPE biodegradation potential by four bacterial isolates (Bacillus safensis FO-36b, Lysinibacillus capsici, Bacillus albus N35-10-2 and Bacillus paranthracis Mn5) and two fungal isolates (Cladosporium halotolerans clone EF_526 and Cladosporium sp. MV-2018B isolate MLT-27). Our study sheds light on the biodegradation of commercial LDPE by soil microorganisms using a novel LDPE-biodegrading additive nanocomposite., Competing Interests: Declaration of Competing Interest ☒ The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier Ltd.)- Published
- 2024
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5. Metal tolerance in enterococci isolated from seabirds in Abrolhos Archipelago, Brazil: Evaluating their role as bioindicators of marine pollution.
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Mocellin RR, Toigo AL, Dos Santos CC, Frazzon J, Nunes GT, Bugoni L, Prichula J, and Frazzon APG
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- Animals, Brazil, Arsenic metabolism, Copper, Mercury metabolism, Metals, Heavy, Enterococcus genetics, Enterococcus isolation & purification, Environmental Monitoring methods, Water Pollutants, Chemical, Birds microbiology
- 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., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)
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- 2024
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6. Global diversity of enterococci and description of 18 previously unknown species.
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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, and Gilmore MS
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- Animals, Humans, Enterococcus genetics, Anti-Bacterial Agents pharmacology, Enterococcus faecalis genetics, Phylogeny, Microbial Sensitivity Tests, Drug Resistance, Bacterial, Enterococcus faecium genetics, Gram-Positive Bacterial Infections
- 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., Competing Interests: Competing interests statement:The authors declare no competing interest.
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- 2024
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7. Anthropic Impact on the Critically Endangered Melanophryniscus admirabilis (Admirable Redbelly Toad): Evidence from the Presence of Multiresistant Enterobacteriaceae.
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Ienes-Lima J, Prichula J, Abadie M, Borges-Martins M, and Frazzon APG
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- Anti-Bacterial Agents pharmacology, Brazil, Disk Diffusion Antimicrobial Tests, Enterobacteriaceae genetics, Agriculture
- Abstract
Melanophryniscus admirabilis is a microendemic and critically endangered toad, known from a single population. This microendemic species inhabits a small fragment of the Atlantic Forest in South Brazil, an area significantly impacted by hydroelectric power plant projects, livestock farming, agricultural activities, biopiracy, and tourism. Given the exclusive and limited population of M. admirabilis, preserving and conserving this species is of utmost importance in Brazil. Research on this species primarily concentrates on its biology, ecology, and ecotoxicology. Currently, there is no knowledge about antimicrobial resistance (AMR) bacteria present in wild M. admirabilis, despite the potential for studying them to provide valuable insights into environmental pollution. To this end, Enterobacteriaceae species (n = 82) obtained from 15 wild M. admirabilis toads were subjected to the standard Kirby-Bauer disk diffusion method to test their AMR. The results showed that Enterobacteriaceae species had the highest antibiotic resistance to IPM (45.1%), CIP (39%), NIT (32.5%), AMP (31.3%), TET (18.3%), and FOX (17%). Of the tested species, 18 (21.9%) species tested were susceptible, 40 (48.8%) were resistant to 1 or 2 different antibiotic classes, and 24 (29.3%) were classified as multidrug-resistant. Overall, our findings suggest that the incidence of AMR in Enterobacteriaceae isolated from wild M. admirabilis is high, indicating environmental stress caused by anthropic pollution in their habit., (© 2023. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)
- Published
- 2023
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8. An affordable and semiautomated approach as a novel strategy for the extraction of DNA using magnetic ionic liquids followed by real time-polymerase chain reaction.
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Ferreira Neto LC, Alves MS, Prichula J, Agnes G, de Oliveira TF, Trentin D, and Merib J
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- DNA, Magnets, Real-Time Polymerase Chain Reaction methods, Magnetic Phenomena, Ionic Liquids
- Abstract
This technical note describes a novel and straightforward experimental strategy for the extraction/capture of DNA using magnetic ionic liquid (MIL) followed by real time-polymerase chain reaction (qPCR) analysis. An affordable and low-cost magneto-based multiwell platform was first examined for capturing DNA allowing for simultaneous extractions that increased the analysis throughput of the experimental workflow. This configuration was composed of a series of neodymium rod magnets attached to a multiwell device in which a magneto-active extraction phase (MIL) was suspended for a single drop microextraction (SDME) approach. In this configuration, up to 32 extractions were able to be performed simultaneously, and DNA was successfully extracted from aqueous samples. Furthermore, as a proof-of-concept, this affordable and simple experimental strategy proved to be efficient for the extraction/capture of DNA from challenging samples such as whole blood without any pretreatment. This fact also consists of important feature compared to previous methodologies that required additional steps of sample preparation.
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- 2023
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9. Global diversity of enterococci and description of 18 novel species.
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Schwartzman JA, Lebreton F, Salamzade R, Martin MJ, Schaufler K, Urhan A, Abeel T, Camargo ILBC, Sgardioli BF, Prichula J, Frazzon APG, Van Tyne D, Treinish G, Innis CJ, Wagenaar JA, Whipple RM, Manson AL, Earl AM, and Gilmore MS
- Abstract
Enterococci are commensal gut microbes of most land animals. They diversified over hundreds of millions of years adapting to evolving hosts and host diets. Of over 60 known enterococcal species, Enterococcus faecalis and E. faecium uniquely emerged in the antibiotic era among leading causes of multidrug resistant hospital-associated infection. The basis for the association of particular enterococcal species with a host is largely unknown. To begin deciphering enterococcal species traits that drive host association, and to assess the pool of Enterococcus -adapted genes from which known facile gene exchangers such as E. faecalis and E. faecium may draw, we collected 886 enterococcal strains from nearly 1,000 specimens representing widely diverse hosts, ecologies and geographies. This provided data on the global occurrence and host associations of known species, identifying 18 new species in the process expanding genus diversity by >25%. The novel species harbor diverse genes associated with toxins, detoxification, and resource acquisition. E. faecalis and E. faecium were isolated from a wide diversity of hosts highlighting their generalist properties, whereas most other species exhibited more restricted distributions indicative of specialized host associations. 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 as well as genes associated with range expansion, such as B-vitamin biosynthesis and flagellar motility. Collectively, this work provides an unprecedentedly broad and deep view of the genus Enterococcus , potential threats to human health, and new insights into its evolution.
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- 2023
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10. First Report of Culturable Skin Bacteria in Melanophryniscus admirabilis (Admirable Redbelly Toad).
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Ienes-Lima J, Prichula J, Abadie M, Borges-Martins M, and Frazzon APG
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- Animals, Bufonidae, Forests, Bacteria, Skin microbiology, Chytridiomycota
- Abstract
Melanophryniscus admirabilis is a small toad, critically endangered with a microendemic distribution in the Atlantic Forest in southern Brazil. The amphibian skin microbiome is considered one of the first lines of defense against pathogenic infections, such as Batrachochytrium dendrobatidis (Bd). The knowledge of skin amphibian microbiomes is important to numerous fields, including species conservation, detection, and quantification of environmental changes and stressors. In the present study, we investigated, for the first time, cultivable bacteria in the skin of wild M. admirabilis, and detected Bd fungus by nested polymerase chain reaction (PCR) technique. Skin swab samples were collected from 15 wild M. admirabilis, and the isolation of bacteria was performed by means of different culture strategies. A total of 62 bacterial isolates being Bacillus (n = 22; 34.48%), Citrobacter (n = 10; 16.13%), and Serratia (n = 12; 19.35%) were more frequently isolated genera. Interestingly, all skin samples tested were Bd negative. Some bacterial genera identified in our study might be acting in a synergic relationship and protecting them against the Bd fungus. In addition, these bacteria may play an essential role in maintaining this species in an environment modulated by anthropic actions. This first report of skin cultivable bacteria from M. admirabilis natural population improves our knowledge of skin amphibian microbiomes, contributing to a better understanding of their ecology and how this species has survived in an environment modulated by anthropic action., (© 2022. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)
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- 2023
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11. Genomic evidence of SARS-CoV-2 reinfection cases in southern Brazil.
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Varela APM, Sant'Anna FH, Dos Santos AV, Prichula J, Comerlato J, Dos Santos GT, and Wendland E
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- Humans, Reinfection, Brazil epidemiology, Phylogeny, Genomics, SARS-CoV-2 genetics, COVID-19
- Abstract
Cases of reinfection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been reported worldwide. We investigated reinfection cases in a set of more than 30,000 samples, and the SARS-CoV-2 genomes from selected samples from four patients with at least two positive diagnoses with an interval ≥ 45 days between tests were sequenced and analyzed. Comparative genomic and phylogenetic analysis confirmed three reinfection cases and suggested that the fourth one was caused by a virus of the same lineage. Viral sequencing is crucial for understanding the natural course of reinfections and for planning public health strategies for management of COVID-19., (© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Austria, part of Springer Nature.)
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- 2023
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12. Evolution of the spontaneous sourdoughs microbiota prepared with organic or conventional whole wheat flours from South Brazil.
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Costa LFX, Kothe CI, Grassotti TT, Garske RP, Sandoval BN, Varela APM, Prichula J, Frazzon J, Mann MB, Thys RCS, and Frazzon APG
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- Triticum, RNA, Ribosomal, 16S genetics, Brazil, Bacteria genetics, Saccharomyces cerevisiae, Fermentation, Flour analysis, Microbiota genetics
- Abstract
The purpose of this study was to compare the composition and stability of bacteria and fungi communities during the propagation of sourdoughs prepared with organic or conventional whole wheat (Triticum aestivum) flours from South Brazil. Sourdoughs were prepared and samples were collected during different fermentation times (0 to 216 h). Total DNA of sourdough samples were extracted and the 16S rRNA gene and Internal Transcribed Spacer region were sequenced by MiSeq-Illumina. A total of 43 and 56 OTUs were identified and defined as core taxa in the bacterial and fungal communities, respectively. The analysis revealed increases in the relative abundances of the lactic acid (Pediococcus pentosaceus, Weissella hellenica and Limosilactobacillus pontis) and acetic acid bacteria (Gluconobacter frateurii and Acetobacter tropicalis) during the sourdough propagation. The filaments fungi, Alternaria tenuissima, Fusarium culmorum, Fusarium petersiae and Microdochium seminicola remained more stable in organic than conventional during propagation cycles. After 216 h of fermentation, both sourdoughs were dominated by acid- and salt-tolerant yeast Issatchenkia orientalis (syn Pichia kudriavzevii, and Candida glycerinogenes). In conclusion, there were no significant differences in microbial communities among the sourdough samples. This study revealed that both flours contain autochthonous LAB, AAB, and yeasts with biotechnological applications in sourdough bread-making.
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- 2022
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13. Hydrocarbon-based plastics: Progress and perspectives on consumption and biodegradation by insect larvae.
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Pivato AF, Miranda GM, Prichula J, Lima JEA, Ligabue RA, Seixas A, and Trentin DS
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- Animals, Biodegradation, Environmental, Hydrocarbons, Insecta, Larva, Plastics, Tenebrio
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The obvious contrast between the remarkable durability and the high consumption of plastic products leads to the deposition of at least 100 million tons of plastics per year in nature. Since 2010, several studies have shown the potential of insect larvae to biodegrade different types of plastics, at higher rates than those reported for microorganisms. This review discusses a compilation of studies about the consumption and biodegradation of hydrocarbon-based plastics, particularly PE, PS, PP and PVC, by lepidopteran and coleopteran larvae. Insects of the Coleoptera order seem to have a better adaptation for PS biodegradation, while those of the Lepidoptera order can better biodegrade PE. Tenebrio molitor biomineralize PE and PS into CO
2 , and PVC into HCl; while Tenebrio obscurus and Zophobas atratus converts PE and PS into CO2 , respectively. Plastic biodegradation by T. molitor has been shown to be dependent on microbiota, exception for PE. Similar PS and PE biodegradation profile has been shown for T. obscurus. PS, PP and PE biodegradation by Z. atratus is also reported to be microbial-dependent. For Galleria mellonella, microbial role on PE biodegradation is still controversial, but the PS metabolism was proved to be microbiota-independent. Advances in this field has stimulated new studies with other insect species, which need to be better explored. Uncovering and understanding the chemical processes behind the innate plastic biodegradation by insect larvae will open the perspective to new eco-friendly innovative biotechnological solutions for the challenge of plastic waste., (Copyright © 2022 Elsevier Ltd. All rights reserved.)- Published
- 2022
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14. Genomic analysis of Enterococcus durans LAB18S, a potential probiotic strain isolated from cheese.
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Comerlato CB, Prichula J, Siqueira FM, Ritter AC, Varela APM, Mayer FQ, and Brandelli A
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Gut microbiota exerts a fundamental role in human health and increased evidence supports the beneficial role of probiotic microorganisms in the maintenance of intestinal health. Enterococcus durans LAB18S was previously isolated from soft cheese and showed some desirable in vitro probiotic properties, for that reason its genome was sequenced and evaluated for genes that can be relevant for probiotic activity and are involved in selenium metabolism. Genome sequencing was performed using the Illumina MiSeq System. A variety of genes potentially associated with probiotic properties, including adhesion capability, viability at low pH, bile salt resistance, antimicrobial activity, and utilization of prebiotic fructooligosaccharides (FOS) were identified. The strain showed tolerance to acid pH and bile salts, exhibited antimicrobial activity and thrived on prebiotic oligosaccharides. Six genes involved in selenium metabolism were predicted. Analysis of the SECIS element showed twelve known selenoprotein candidates. E. durans LAB18S was the only food isolate showing absence of plasmids, virulence and antimicrobial resistance genes, when compared with other 30 E. durans genomes. The results of this study provide evidence supporting the potential of E. durans LAB18S as alternative for probiotic formulations.
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- 2022
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15. Emergence of the novel SARS-CoV-2 lineage VUI-NP13L and massive spread of P.2 in South Brazil.
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Sant'Anna FH, Muterle Varela AP, Prichula J, Comerlato J, Comerlato CB, Roglio VS, Mendes Pereira GF, Moreno F, Seixas A, and Wendland EM
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- Brazil epidemiology, COVID-19 epidemiology, Genetic Variation, Genome, Viral, Humans, Phylogeny, SARS-CoV-2 genetics, COVID-19 virology, SARS-CoV-2 classification, SARS-CoV-2 isolation & purification
- Abstract
In this study, we analyzed 340 whole genomes of SARS-CoV-2, which were sampled between April and November 2020 in 33 cities of Rio Grande do Sul, South Brazil. We demonstrated the circulation of two novel emergent lineages, VUI-NP13L and VUI-NP13L-like, and five major lineages that had already been assigned (B.1.1.33, B.1.1.28, P.2, B.1.91, B.1.195). P.2 and VUI-NP13L demonstrated a massive spread in October 2020. Constant and consistent genomic surveillance is crucial to identify newly emerging SARS-CoV-2 lineages in Brazil and to guide decision making in the Brazilian Public Healthcare System.
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- 2021
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16. SARS-CoV-2 introduction and lineage dynamics across three epidemic peaks in Southern Brazil: massive spread of P.1.
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Varela APM, Prichula J, Mayer FQ, Salvato RS, Sant'Anna FH, Gregianini TS, Martins LG, Seixas A, and Veiga ABGD
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- Adolescent, Adult, Aged, Aged, 80 and over, Brazil epidemiology, COVID-19 transmission, Child, Child, Preschool, Cities epidemiology, Female, Genome, Viral, Humans, Infant, Male, Middle Aged, Mutation, SARS-CoV-2 isolation & purification, Spike Glycoprotein, Coronavirus genetics, Viral Proteins genetics, Young Adult, COVID-19 epidemiology, COVID-19 virology, Phylogeny, SARS-CoV-2 genetics
- Abstract
Genomic surveillance of SARS-CoV-2 is paramount for understanding viral dynamics, contributing to disease control. This study analyzed SARS-CoV-2 genomic diversity in Rio Grande do Sul (RS), Brazil, including the first reported case in each Regional Health Coordination and cases from three epidemic peaks. Ninety SARS-CoV-2 genomes from RS were sequenced and analyzed through comparison with SARS-CoV-2 datasets available in GISAID for phylogenetic inference and mutation analysis. Among the first reported cases, we found the following lineages: B.1 (33.3%), B.1.1.28 (26.7%), B.1.1 (13.3%), B.1.1.33 (10.0%), and A (6.7%), evidencing SARS-CoV-2 introduction by both international origin and community-driven transmission. We found predominance of B.1.1.33 (50.0%) and B.1.1.28 (35.0%) during the first epidemic peak (July-August 2020), emergence of P.2 (55.6%) in the second peak (November-December 2020), and massive spread of P.1 and related sequences (78.4%), such as P.1-like-II, P.1.1 and P.1.2 in the third peak (February-April, 2021). Eighteen novel mutation combinations were found among P.1 genomes, and 22 different spike mutations and/or deletions among P.1 and related sequences. This study shows the dispersion of SARS-CoV-2 lineages in Southern Brazil and describes SARS-CoV-2 diversity during three epidemic peaks, highlighting the spread of P.1 and the high genetic diversity of currently circulating lineages. Genomic monitoring of SARS-CoV-2 is essential to guide health authorities' decisions to control COVID-19 in Brazil., (Copyright © 2021 The Authors. Published by Elsevier B.V. All rights reserved.)
- Published
- 2021
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17. Fecal bacterial communities of wild black capuchin monkeys ( Sapajus nigritus ) from the Atlantic Forest biome in Southern Brazil are divergent from those of other non-human primates.
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Grassotti TT, Kothe CI, Prichula J, Mohellibi N, Mann MB, Wagner PGC, Campos FS, Campos AAS, Frazzon J, and Frazzon APG
- Abstract
Gut microbiota are influenced by factors such as diet, habitat, and social contact, which directly affect the host's health. Studies related to gut microbiota in non-human primates are increasing worldwide. However, little remains known about the gut bacterial composition in wild Brazilian monkeys. Therefore, we studied the fecal microbiota composition of wild black capuchin monkey ( Sapajus nigritus ) (n=10) populations from two different Atlantic Forest biome fragments (five individuals per fragment) in south Brazil. The bacterial community was identified via the high-throughput sequencing and partial amplification of the 16S rRNA gene (V4 region) using an Ion Personal Genome Machine (PGM
TM ) System. In contrast to other studies involving monkey microbiota, which have generally reported the phyla Firmicutes and Bacteroidetes as predominant, black capuchin monkeys showed a high relative abundance of Proteobacteria ( χ ¯ = 80.54%), followed by Firmicutes ( χ ¯ = 12.14%), Actinobacteria ( χ ¯ = 4.60%), and Bacteriodetes ( χ ¯ = 1.31%). This observed particularity may have been influenced by anthropogenic actions related to the wild habitat and/or diet specific to the Brazilian biome's characteristics and/or monkey foraging behavior. Comparisons of species richness (Chao1) and diversity indices (Simpson and InvSimpson) showed no significant differences between the two groups of monkeys. Interestingly, PICRUSt2 analysis revealed that metabolic pathways present in the bacterial communities were associated with xenobiotic biodegradation and the biosynthesis of secondary metabolites, which may suggest positive effects on monkey health and conservation in this anthropogenic habitat. Infectious disease-associated microorganisms were also observed in the samples. The present study provides information about the bacterial population and metabolic functions present in fecal microbiota, which may contribute to a better understanding of the ecology and biology of black capuchin monkeys living in forest fragments within the Atlantic Forest biome in southern Brazil. Additionally, the present study demonstrates that the fecal bacterial communities of wild black capuchin monkeys in this area are divergent from those of other wild non-human primates., Competing Interests: None to be declared., (© 2021 The Authors. Published by Elsevier B.V.)- Published
- 2021
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18. Genome Mining for Antimicrobial Compounds in Wild Marine Animals-Associated Enterococci.
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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, and Gilmore MS
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- Animals, Bacteriocins classification, Bacteriocins metabolism, Computational Biology, Enterococcus metabolism, Feces microbiology, Multigene Family, Animals, Wild microbiology, Anti-Infective Agents metabolism, Aquatic Organisms microbiology, Bacteriocins genetics, Enterococcus genetics, Probiotics metabolism, Terpenes classification, Terpenes metabolism
- 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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- 2021
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19. The Oral Bacterial Community in Melanophryniscus admirabilis (Admirable Red-Belly Toads): Implications for Conservation.
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Mann MB, Prichula J, de Castro ÍMS, Severo JM, Abadie M, De Freitas Lima TM, Caorsi V, Borges-Martins M, Frazzon J, and Frazzon APG
- Abstract
Melanophryniscus admirabilis (admirable red-belly toad) is a microendemic and critically endangered species found exclusively along 700 m of the Forqueta River, in a fragment of the Atlantic Forest of southern Brazil. One of the greatest concerns regarding the conservation of this species is the extensive use of pesticides in areas surrounding their natural habitat. In recent years, the adaptation and persistence of animal species in human-impacted environments have been associated with microbiota. Therefore, the present study aimed to characterize the oral bacterial community of wild M. admirabilis and to address the question of how this community might contribute to this toad's adaptation in the anthropogenic environment as well as its general metabolic capabilities. A total of 11 oral samples collected from wild M. admirabilis were characterized and analyzed via high-throughput sequencing. Fragments of the 16S rRNA variable region 4 (V4) were amplified, and sequencing was conducted using an Ion Personal Genome Machine (PGM) System with 316 chips. A total of 181,350 sequences were obtained, resulting in 16 phyla, 34 classes, 39 orders, and 77 families. Proteobacteria dominated (53%) the oral microbiota of toads, followed by Firmicutes (18%), Bacteroidetes (17%), and Actinobacteria (5%). No significant differences in microbial community profile from among the samples were reported, which suggests that the low dietary diversity observed in this population may directly influence the bacterial composition. Inferences of microbiome function were performed using PICRUSt2 software. Important pathways (e.g., xenobiotic degradation pathways for pesticides and aromatic phenolic compounds) were detected, which suggests that the bacterial communities may serve important roles in M. admirabilis health and survival in the anthropogenic environment. Overall, our results have important implications for the conservation and management of this microendemic and critically endangered species.
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- 2021
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20. Enterococci from Wild Magellanic Penguins (Spheniscus magellanicus) as an Indicator of Marine Ecosystem Health and Human Impact.
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Prichula J, Van Tyne D, Schwartzman J, Sant'Anna FH, Pereira RI, da Cunha GR, Tavares M, Lebreton F, Frazzon J, d'Azevedo PA, Seixas A, Frazzon APG, and Gilmore MS
- Subjects
- Animals, Brazil, Ecosystem, Enterococcus isolation & purification, Environmental Biomarkers, Spheniscidae microbiology
- Abstract
Enterococci are commensals that proliferated as animals crawled ashore hundreds of millions of years ago. They are also leading causes of multidrug-resistant hospital-acquired infections. While most studies are driven by clinical interest, comparatively little is known about enterococci in the wild or the effect of human activity on them. Pharmaceutical pollution and runoff from other human activities are encroaching widely into natural habitats. To assess their reach into remote habitats, we investigated the identity, genetic relatedness, and presence of specific traits among 172 enterococcal isolates from wild Magellanic penguins. Four enterococcal species, 18 lineage groups, and different colonization patterns were identified. One Enterococcus faecalis lineage, sequence type 475 (ST475), was isolated from three different penguins, making it of special interest. Its genome was compared to those of other E. faecalis sequence types (ST116 and ST242) recovered from Magellanic penguins, as well as to an existing phylogeny of E. faecalis isolated from diverse origins over the past 100 years. No penguin-derived E. faecalis strains were closely related to dominant clinical lineages. Most possessed intact CRISPR defenses, few mobile elements, and antibiotic resistances limited to those intrinsic to the species and lacked pathogenic features conveyed by mobile elements. Interestingly, plasmids were identified in penguin isolates that also had been reported for other marine mammals. Enterococci isolated from penguins showed limited anthropogenic impact, indicating that they are likely representative of those naturally circulating in the ecosystem inhabited by the penguins. These findings establish an important baseline for detecting the encroachment of human activity into remote planetary environments. IMPORTANCE Enterococci are host-associated microbes that have an unusually broad range, from the built hospital environment to the guts of insects and other animals in remote locations. Despite their occurrence in the guts of animals for hundreds of millions of years, we know little about the properties that confer this range or how anthropogenic activities may be introducing new selective forces. Magellanic penguins live at the periphery of human habitation. It was of interest to examine enterococci from these animals for the presence of antibiotic resistance and other markers reflective of anthropogenic selection. Diverse enterococcal lineages found discount the existence of a single well-adapted intrinsic penguin-specific species. Instead, they appear to be influenced by a carnivorous lifestyle and enterococci present in the coastal sea life consumed. These results indicate that currently, the penguin habitat remains relatively free of pollutants that select for adaptation to human-derived stressors., (Copyright © 2020 American Society for Microbiology.)
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- 2020
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21. Corrigendum "Resistance to antimicrobial agents among enterococci isolated from fecal samples of wild marine species in the southern coast of Brazil" [Mar. Pollut. Bull. 105 (2016) 51-57].
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Prichula J, Pereira RI, Wachholz GR, Cardoso LA, Tolfo NCC, Santestevan NA, Medeiros AW, Tavares M, Frazzon J, d'Azevedo PA, and Frazzon APG
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- 2019
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22. Draft Genome Sequence of Enterococcus faecalis Strain F165 Isolated from a Urinary Tract Infection.
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Paim TG, Pieta L, Prichula J, Sambrano GE, Soares R, Bello AD, Frazzon J, and d'Azevedo PA
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We report here a draft genome sequence of Enterococcus faecalis strain F165 isolated from a urine specimen in South Brazil. The genome size was 3,049,734 bp, with a G+C content of 37.38%, and genes related to antimicrobial resistance and adherence were found in the strain. These findings are consistent with pathogenesis of E. faecalis species., (Copyright © 2016 Paim et al.)
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- 2016
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23. Draft Genome Sequence of Brazilian Escherichia coli Uropathogenic Strain E2.
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Paim TG, Pieta L, Prichula J, Sambrano GE, Soares R, Caierão J, Frazzon J, and d'Azevedo PA
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Escherichia coli is a common pathogen recovered from cystitis infections. In this report, we announce the draft genome sequence of strain E2 isolated from the urine specimen from a female patient in South Brazil. The genome assembly has 5,081,209 bp, a G+C content of 50.57%, and virulence factors associated with both enteroaggregative and uropathogenic E. coli strains., (Copyright © 2016 Paim et al.)
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- 2016
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24. Resistance to antimicrobial agents among enterococci isolated from fecal samples of wild marine species in the southern coast of Brazil.
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Prichula J, Pereira RI, Wachholz GR, Cardoso LA, Tolfo NC, Santestevan NA, Medeiros AW, Tavares M, Frazzon J, d'Azevedo PA, and Frazzon AP
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- Animals, Anti-Bacterial Agents pharmacology, Brazil, Drug Resistance, Microbial, Enterococcus isolation & purification, Enterococcus faecalis genetics, Enterococcus faecium genetics, Environmental Monitoring, Microbial Sensitivity Tests, Polymerase Chain Reaction, Aquatic Organisms microbiology, Drug Resistance, Bacterial genetics, Feces microbiology
- Abstract
The purpose of this study was to evaluate species distribution, antimicrobial resistance profiles, and presence of resistance genes in enterococci isolated from fecal samples of wild marine species, including seabirds (n=12), sea turtles (n=8), and mammals (n=3) found alive or dead in southern coast of Brazil. Enterococci were classified based on phenotypic and genotypic characteristics, tested for antibiotic susceptibility, and the presence of tet(S), tet(M), tet(L), mrsC, and erm(B) genes by PCR. Enterococcus faecalis and Enterococcus faecium were the most common species. Single (37.09%), double (25.80%), and multiple (16.12%) antibiotic resistance patterns were observed. Resistance to rifampicin occurred most frequently. The msrC, tet(M), and/or tet(L) genes were detected in 60.15%, 73.07%, and 23.07% of the resistant strains, respectively. In conclusion, the presence of antibiotic resistant strains in these species could be related to food web interactions and aquatic pollutants or linked to environmental resistome., (Copyright © 2016 Elsevier Ltd. All rights reserved.)
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- 2016
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25. Complete Genome Sequence of Enterococcus faecalis Strain P8-1 Isolated from Wild Magellanic Penguin (Spheniscus magellanicus) Feces on the South Coast of Brazil.
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Prichula J, Campos FS, Pereira RI, Cardoso LA, Wachholz GR, Pieta L, Mariot RF, de Moura TM, Tavares M, d'Azevedo PA, Frazzon J, and Frazzon AP
- Abstract
Enterococcus faecalis strains have a ubiquitous nature that allows them to survive in different niches. Studies involving enterococci isolated from marine animals are scarce. Therefore, in this study, we report the complete genome sequence of E. faecalis strain P8-1 isolated from feces of a Magellanic penguin on the south coast of Brazil., (Copyright © 2016 Prichula et al.)
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- 2016
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26. Complete Genome Sequences of Two Listeria monocytogenes Serovars, 1/2a and 4b, Isolated from Dairy Products in Brazil.
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Pieta L, Campos FS, Mariot RF, Prichula J, de Moura TM, Frazzon AP, and Frazzon J
- Abstract
Listeria monocytogenes is the foodborne pathogen responsible for a bacterial infection called listeriosis. Here, we present the whole-genome sequences of two L. monocytogenes serovars, 1/2a and 4b, which are considered the most prevalent in food processing plants and listeriosis outbreaks, respectively., (Copyright © 2015 Pieta et al.)
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- 2015
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27. Antimicrobial resistance and virulence factor gene profiles of Enterococcus spp. isolates from wild Arctocephalus australis (South American fur seal) and Arctocephalus tropicalis (Subantarctic fur seal).
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Santestevan NA, de Angelis Zvoboda D, Prichula J, Pereira RI, Wachholz GR, Cardoso LA, de Moura TM, Medeiros AW, de Amorin DB, Tavares M, d'Azevedo PA, Franco AC, Frazzon J, and Frazzon AP
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- Animals, Animals, Wild microbiology, Brazil, Drug Resistance, Bacterial, Enterococcus isolation & purification, Enterococcus pathogenicity, Enterococcus faecalis classification, Enterococcus faecalis drug effects, Enterococcus faecalis isolation & purification, Feces microbiology, Genes, Bacterial, Genotype, Microbial Sensitivity Tests, Phylogeny, Random Amplified Polymorphic DNA Technique, Virulence genetics, Virulence Factors genetics, Anti-Bacterial Agents pharmacology, Enterococcus drug effects, Enterococcus genetics, Fur Seals microbiology
- Abstract
Enterococci are natural inhabitants of the gastrointestinal tracts in humans and animals. Epidemiological data suggest that enterococci are important reservoirs of antimicrobial resistant genes that may be transmitted from other bacterial species The aim of this study was to investigate the species composition, antimicrobial resistance and virulence genes in enterococci recovered from fecal samples of wild Arctocephalus australis and A. tropicalis found dead along the South Coast of Brazil. From a total of 43 wild fur seals, eleven were selected for this study. Phenotypic and genotypic characterizations were used to classify Enterococcus species. Strains were tested for susceptibility to 10 antibiotics, presence of ace, gelE, asa, cylA, tet(L), tet(M) and erm(B) genes by PCR, and genetic variability using RAPD-PCR. Among the 50 enterococci isolated, 40% were Enterococcus faecalis, 40% E. hirae, 12% E. casseliflavus and 8 % other enterococcal species. Resistance profiles were observed to erythromycin, nitrofurantoin, tetracycline, norfloxacin and ciprofloxacin. The prevalence of virulence genes was ace (68%), gelE (54%), asa (22%) and cylA (4%). In erythromycin- and tetracycline strains, erm(B) and tet(M) were detected, respectively. The RAPD-PCR demonstrated a close phylogenetic relationship between the enterococci isolated from A. australis and A. tropicalis. In conclusion, different enterococcus species showing antimicrobial resistance and virulence determinates were isolated from fecal samples of fur seals. Antibiotic resistant strains in these animals could be related within food chain and aquatic pollutants or linked to environmental resistome, and demonstrates the potential importance of these animals as reservoirs and disseminators of such determinants in marine environmental.
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- 2015
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