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de Oliveira Moraes P, da Silva Pires PG, Benetti Filho V, Lima ALF, Kindlein L, Taschetto D, Favero A, Wagner G. Intestinal health of broilers challenged with Eimeria spp. using functional oil blends in two physical forms with or without anticoccidials. Sci Rep 2023; 13:14612. [PMID: 37670021 PMCID: PMC10480430 DOI: 10.1038/s41598-023-41743-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 08/30/2023] [Indexed: 09/07/2023] Open
Abstract
This study aimed to assess the impact of a commercial blend of functional oils, specifically cashew nutshell liquid and castor oil (FO), in two physical forms (solid: P; liquid: S), in comparison to a combination of virginiamycin and anticoccidials on the gut health of broilers challenged with coccidiosis. A total of 1760 1-day-old male chicks were randomly distributed in a study design with eight treatments. The treatments included: a control group (without additive), OFS_0.75_kg/t (FO spray), OFP_1.0_kg/t (FO powder), OFP_1.5_kg/t (FO liquid spray), Sal (anticoccidials), Sal_Vir (virginiamycin and anticoccidials), Sal_OFS_0.5_ kg/t (anticoccidials plus FO spray), and Sal_OFP_1.0_kg/t (anticoccidials plus FO powder). All birds were challenged with Eimeria spp. at 14 days. The physical form of FO did not affect performance and intestinal health parameters. At 42 days, broilers from the control and OFS_0.75 treatments were the lightest, while those from the Sal_Vir and Sal_OFP_1.0 treatments were the heaviest (P < 0.05). FO reduced the presence of Clostridium perfringens. The individual phytogenic additives did not prevent weight loss in birds challenged with Eimeria, but they mitigated the effects of the infection by modulating the intestinal microbiota. A synergistic effect was observed between the FO and anticoccidials, yielding satisfactory results in substituting virginiamycin.
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Affiliation(s)
- Priscila de Oliveira Moraes
- Department of Animal Science and Rural Development, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil.
| | | | - Vilmar Benetti Filho
- Laboratory of Bioinformatics, Center of Biological Sciences, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - André Luís Ferreira Lima
- Department of Animal Science and Rural Development, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Liris Kindlein
- Department of Preventive Veterinary Medicine, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, 91540-000, Brazil
| | | | - André Favero
- Santa Livia Farm, Farroupilha, Rio Grande do Sul, Brazil
| | - Glauber Wagner
- Laboratory of Bioinformatics, Center of Biological Sciences, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
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Pilati GVT, Cadamuro RD, Filho VB, Dahmer M, Elois MA, Savi BP, Salles GBC, Muniz EC, Fongaro G. Bacteriophage-Associated Antimicrobial Resistance Genes in Avian Pathogenic Escherichia coli Isolated from Brazilian Poultry. Viruses 2023; 15:1485. [PMID: 37515172 PMCID: PMC10386125 DOI: 10.3390/v15071485] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/30/2023] Open
Abstract
Colibacillosis is a disease caused by Escherichia coli and remains a major concern in poultry production, as it leads to significant economic losses due to carcass condemnation and clinical symptoms. The development of antimicrobial resistance is a growing problem of worldwide concern. Lysogenic bacteriophages are effective vectors for acquiring and disseminating antibiotic resistance genes (ARGs). The aim of this study was to investigate the complete genome of Escherichia coli isolates from the femurs of Brazilian broiler chickens in order to investigate the presence of antimicrobial resistance genes associated with bacteriophages. Samples were collected between August and November 2021 from broiler batches from six Brazilian states. Through whole genome sequencing (WGS), data obtained were analyzed for the presence of antimicrobial resistance genes. Antimicrobial resistance genes against the aminoglycosides class were detected in 79.36% of the isolates; 74.6% had predicted sulfonamides resistance genes, 63.49% had predicted resistance genes against β-lactams, and 49.2% of the isolates had at least one of the tetracycline resistance genes. Among the detected genes, 27 have been described in previous studies and associated with bacteriophages. The findings of this study highlight the role of bacteriophages in the dissemination of ARGs in the poultry industry.
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Affiliation(s)
- Giulia Von Tönnemann Pilati
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
| | - Rafael Dorighello Cadamuro
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
| | - Vilmar Benetti Filho
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
| | - Mariane Dahmer
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
| | - Mariana Alves Elois
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
| | - Beatriz Pereira Savi
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
| | - Gleidson Biasi Carvalho Salles
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
- Zoetis Industry of Veterinary Products LTDA, São Paulo 04709-111, Brazil
| | | | - Gislaine Fongaro
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
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Padilha DA, Souza DSM, Kawagoe EK, Filho VB, Amorim AN, Barazzetti FH, Schörner MA, Fernandes SB, Coelho BK, Rovaris DB, Dos Anjos MPD, Moser JR, Melo FR, De Souza BB, Bessa DDC, Mendes FHDPES, Boing AC, Boing AF, Lacerda JTD, Moura GV, Bastiani DCD, Moraes MHD, De Oliveira LFV, Moreira RS, Stoco PH, Bazzo ML, Fongaro G, Wagner G. Genomic Surveillance of SARS-CoV-2 in Healthcare Workers: A Critical Sentinel Group for Monitoring the SARS-CoV-2 Variant Shift. Viruses 2023; 15:v15040984. [PMID: 37112964 PMCID: PMC10146896 DOI: 10.3390/v15040984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/11/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
SARS-CoV-2 genome surveillance is important for monitoring risk groups and health workers as well as data on new cases and mortality rate due to COVID-19. We characterized the circulation of SARS-CoV-2 variants from May 2021 to April 2022 in the state of Santa Catarina, southern Brazil, and evaluated the similarity between variants present in the population and healthcare workers (HCW). A total of 5291 sequenced genomes demonstrated the circulation of 55 strains and four variants of concern (Alpha, Delta, Gamma and Omicron-sublineages BA.1 and BA.2). The number of cases was relatively low in May 2021, but the number of deaths was higher with the Gamma variant. There was a significant increase in both numbers between December 2021 and February 2022, peaking in mid-January 2022, when the Omicron variant dominated. After May 2021, two distinct variant groups (Delta and Omicron) were observed, equally distributed among the five Santa Catarina mesoregions. Moreover, from November 2021 to February 2022, similar variant profiles between HCW and the general population were observed, and a quicker shift from Delta to Omicron in HCW than in the general population. This demonstrates the importance of HCW as a sentinel group for monitoring disease trends in the general population.
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Affiliation(s)
- Dayane Azevedo Padilha
- Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis 88040-900, Santa Catarina, Brazil
| | - Doris Sobral Marques Souza
- Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis 88040-900, Santa Catarina, Brazil
| | - Eric Kazuo Kawagoe
- Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis 88040-900, Santa Catarina, Brazil
| | - Vilmar Benetti Filho
- Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis 88040-900, Santa Catarina, Brazil
| | - Ariane Nicaretta Amorim
- Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis 88040-900, Santa Catarina, Brazil
| | - Fernando Hartmann Barazzetti
- Centro de Ciências da Saúde, Universidade Federal de Santa Catarina, Florianópolis 88040-370, Santa Catarina, Brazil
| | - Marcos André Schörner
- Centro de Ciências da Saúde, Universidade Federal de Santa Catarina, Florianópolis 88040-370, Santa Catarina, Brazil
| | - Sandra Bianchini Fernandes
- Laboratório Central do Estado da Saúde de Santa Catarina, Florianópolis 88010-001, Santa Catarina, Brazil
| | - Bruna Kellet Coelho
- Laboratório Central do Estado da Saúde de Santa Catarina, Florianópolis 88010-001, Santa Catarina, Brazil
| | - Darcita Buerger Rovaris
- Laboratório Central do Estado da Saúde de Santa Catarina, Florianópolis 88010-001, Santa Catarina, Brazil
| | | | - Juliana Righetto Moser
- Diretoria de Vigilância Epidemiológica de Santa Catarina, Florianópolis 88015-130, Santa Catarina, Brazil
| | - Fernanda Rosene Melo
- Diretoria de Vigilância Epidemiológica de Santa Catarina, Florianópolis 88015-130, Santa Catarina, Brazil
| | | | - Dimitri da Costa Bessa
- Diretoria de Vigilância Epidemiológica de Santa Catarina, Florianópolis 88015-130, Santa Catarina, Brazil
| | | | - Alexandra Crispim Boing
- Centro de Ciências da Saúde, Universidade Federal de Santa Catarina, Florianópolis 88040-370, Santa Catarina, Brazil
| | - Antonio Fernando Boing
- Centro de Ciências da Saúde, Universidade Federal de Santa Catarina, Florianópolis 88040-370, Santa Catarina, Brazil
| | - Josimari Telino de Lacerda
- Centro de Ciências da Saúde, Universidade Federal de Santa Catarina, Florianópolis 88040-370, Santa Catarina, Brazil
| | - Guilherme Valle Moura
- Centro de Sócio Econômico, Universidade Federal de Santa Catarina, Florianópolis 88040-900, Santa Catarina, Brazil
| | | | | | | | | | - Patricia Hermes Stoco
- Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis 88040-900, Santa Catarina, Brazil
| | - Maria Luiza Bazzo
- Centro de Ciências da Saúde, Universidade Federal de Santa Catarina, Florianópolis 88040-370, Santa Catarina, Brazil
| | - Gislaine Fongaro
- Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis 88040-900, Santa Catarina, Brazil
| | - Glauber Wagner
- Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis 88040-900, Santa Catarina, Brazil
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Sielski Galvão Soares L, Casella T, Kawagoe EK, Benetti Filho V, Omori WP, Nogueira MCL, Wagner G, Rodrigues de Oliveira R, Stahlhofer SR, Antunes Ferreira F, Tondo EC, De Dea Lindner J. Phenotypic and genotypic characterization of antibiotic resistance of Salmonella Heidelberg in the south of Brazil. Int J Food Microbiol 2023; 391-393:110151. [PMID: 36871395 DOI: 10.1016/j.ijfoodmicro.2023.110151] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/20/2023] [Accepted: 02/22/2023] [Indexed: 03/03/2023]
Abstract
Salmonella is the main human pathogen present in the poultry chain. Salmonella Heidelberg is one of the most important serovars for public health since it has been frequently isolated in broiler chickens from different countries and may present multidrug resistance (MDR). This study was carried out with 130 S. Heidelberg isolates collected from pre-slaughter broiler farms in 2019 and 2020 in 18 cities from three Brazilian states to study relevant aspects regarding their genotypic and phenotypic resistance. The isolates were tested and identified using somatic and flagellar antiserum (0:4, H:2, and H:r), and an antimicrobial susceptibility test (AST) was performed against 11 antibiotics for veterinary use. The strains were typed by Enterobacterial Repetitive Intergenic Consensus (ERIC)-PCR, and representatives of the main clusters of the identified profiles were sequenced by Whole Genome Sequencing (WGS). AST results showed that all isolates were resistant to sulfonamide, 54 % (70/130) were resistant to amoxicillin, and only one was sensitive to tetracycline. Twelve isolates (15.4 %) were MDR. The dendrogram obtained from the ERIC-PCR showed that the strains were grouped into 27 clusters with similarity above 90 %, with some isolates showing 100 % similarity but with different phenotypic profiles of antimicrobial resistance. Identical strains collected on the same farm on other dates were identified, indicating that they were residents. WGS identified 66 antibiotic-resistance genes. The sul2 (present in all sequenced samples) and tet(A) genes were highlighted and validated in the experimental analysis. The fosA7 gene was also identified in all sequenced samples, but resistance was not observed in the phenotypic test, possibly due to the heteroresistance of the S. Heidelberg strains evaluated. Considering that chicken meat is one of the most consumed meats in the world, the data obtained in the present study can corroborate the mapping of the origin and trends of antimicrobial resistance.
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Affiliation(s)
- Luana Sielski Galvão Soares
- Food Technology and Bioprocess Research Group, Department of Food Science and Technology, Federal University of Santa Catarina (UFSC), Florianópolis, SC, Brazil
| | - Tiago Casella
- Center for Microorganisms Investigation, São José Do Rio Preto Medical School (FAMERP), São José Do Rio Preto, SP, Brazil
| | - Eric Kazuo Kawagoe
- Laboratory of Bioinformatics, Department of Microbiology, Immunology and Parasitology, UFSC, Florianópolis, SC, Brazil
| | - Vilmar Benetti Filho
- Laboratory of Bioinformatics, Department of Microbiology, Immunology and Parasitology, UFSC, Florianópolis, SC, Brazil
| | | | - Mara Corrêa Lelles Nogueira
- Center for Microorganisms Investigation, São José Do Rio Preto Medical School (FAMERP), São José Do Rio Preto, SP, Brazil
| | - Glauber Wagner
- Laboratory of Bioinformatics, Department of Microbiology, Immunology and Parasitology, UFSC, Florianópolis, SC, Brazil
| | | | | | | | - Eduardo Cesar Tondo
- Laboratory of Food Microbiology and Food Control, Institute of Food Science and Food Technology of Federal University of Rio Grande do Sul (ICTA/UFRGS), Porto Alegre, RS, Brazil
| | - Juliano De Dea Lindner
- Food Technology and Bioprocess Research Group, Department of Food Science and Technology, Federal University of Santa Catarina (UFSC), Florianópolis, SC, Brazil.
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Moreira RS, Calomeno NA, das Neves GB, do Nascimento LFN, Filho VB, Wagner G, Miletti LC. Trypanosoma evansi secretome carries potential biomarkers for Surra diagnosis. J Proteomics 2023; 272:104789. [PMID: 36464092 DOI: 10.1016/j.jprot.2022.104789] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 11/17/2022] [Accepted: 11/22/2022] [Indexed: 12/03/2022]
Abstract
Trypanosoma evansi is a parasite that is phylogenetically close to Trypanosoma brucei and is the causative agent of a disease known as surra. Surra is responsible for a high mortality rate in livestock and large economic losses in the Americas, Africa, and Asia. This work aimed to analyze in vitro secreted proteins from T. evansi and identify potential treatment and diagnostic biomarkers for surra diagnosis. Two groups were used. In one group the parasites were purified using a DEAE-Cellulose column and maintained in a secretion medium while in the other group the parasites were not purified. Each group was further divided to be maintained at either 37 °C or 27 °C. We identified 246 proteins through mass spectrometry and found that the temperature appears to modulate protein secretion. We found minimal variations in the protein pools from pure and non-purified sets. We observed an emphasis on proteins associated to vesicles, glycolysis, and cellular homeostasis through the enrichment of GO. Also, we found that most secretome proteins share homologous proteins with T. b. brucei, T. b. gambiense, T. vivax, T. equiperdum, and T. b. rhodesiense secretome but unique T. evansi epitopes with potential biomarkers for surra diagnosis were detected. SIGNIFICANCE: Trypanosoma evansi is a parasite of African origin that is phylogenetically close to Trypanosoma brucei. As with other trypanosomatids and blood parasites, its infection causes non-pathognomonic symptoms, which makes its diagnosis difficult. One great problem is the fact that no diagnostic test differentiates between Trypanosoma equiperdum and T. evansi, which is a problem in South America and Asia, and Africa. Thus, it is urgent to study the biochemistry of the parasite to discover proteins that can be used for differential diagnosis or be possible therapeutic targets. In addition, the study of the secretome can point out proteins that are used by the parasite in its interactions with the host, helping to understand the progression of the disease.
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Affiliation(s)
- Renato Simões Moreira
- Laboratório de Hemoparasitas e Vetores, Centro de Ciências Agroveterinárias (CAV), Universidade do Estado de Santa Catarina (UDESC), Av. Luís de Camões, 2090, Conta Dinheiro, Lages, SC 88520-000, Brazil; Instituto Federal de Santa Catarina (IFSC), Campus Gaspar, R. Adriano Kormann, 510 - Bela Vista, Gaspar, SC 89111-009, Brazil
| | - Nathália Anderson Calomeno
- Laboratório de Hemoparasitas e Vetores, Centro de Ciências Agroveterinárias (CAV), Universidade do Estado de Santa Catarina (UDESC), Av. Luís de Camões, 2090, Conta Dinheiro, Lages, SC 88520-000, Brazil
| | - Gabriella Bassi das Neves
- Laboratório de Hemoparasitas e Vetores, Centro de Ciências Agroveterinárias (CAV), Universidade do Estado de Santa Catarina (UDESC), Av. Luís de Camões, 2090, Conta Dinheiro, Lages, SC 88520-000, Brazil
| | - Luiz Flávio Nepomuceno do Nascimento
- Laboratório de Hemoparasitas e Vetores, Centro de Ciências Agroveterinárias (CAV), Universidade do Estado de Santa Catarina (UDESC), Av. Luís de Camões, 2090, Conta Dinheiro, Lages, SC 88520-000, Brazil
| | - Vilmar Benetti Filho
- Laboratório de Bioinformática, Universidade Federal de Santa Catarina, Campus João David Ferreira Lima, Setor F, Bloco A, Sala 318, Caixa postal 476, Trindade, Florianópolis, SC 88040-970, Brazil
| | - Glauber Wagner
- Laboratório de Bioinformática, Universidade Federal de Santa Catarina, Campus João David Ferreira Lima, Setor F, Bloco A, Sala 318, Caixa postal 476, Trindade, Florianópolis, SC 88040-970, Brazil
| | - Luiz Claudio Miletti
- Laboratório de Hemoparasitas e Vetores, Centro de Ciências Agroveterinárias (CAV), Universidade do Estado de Santa Catarina (UDESC), Av. Luís de Camões, 2090, Conta Dinheiro, Lages, SC 88520-000, Brazil.
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Maia GA, Filho VB, Kawagoe EK, Teixeira Soratto TA, Moreira RS, Grisard EC, Wagner G. AnnotaPipeline: An integrated tool to annotate eukaryotic proteins using multi-omics data. Front Genet 2022; 13:1020100. [DOI: 10.3389/fgene.2022.1020100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/11/2022] [Indexed: 11/23/2022] Open
Abstract
Assignment of gene function has been a crucial, laborious, and time-consuming step in genomics. Due to a variety of sequencing platforms that generates increasing amounts of data, manual annotation is no longer feasible. Thus, the need for an integrated, automated pipeline allowing the use of experimental data towards validation of in silico prediction of gene function is of utmost relevance. Here, we present a computational workflow named AnnotaPipeline that integrates distinct software and data types on a proteogenomic approach to annotate and validate predicted features in genomic sequences. Based on FASTA (i) nucleotide or (ii) protein sequences or (iii) structural annotation files (GFF3), users can input FASTQ RNA-seq data, MS/MS data from mzXML or similar formats, as the pipeline uses both transcriptomic and proteomic information to corroborate annotations and validate gene prediction, providing transcription and expression evidence for functional annotation. Reannotation of the available Arabidopsis thaliana, Caenorhabditis elegans, Candida albicans, Trypanosoma cruzi, and Trypanosoma rangeli genomes was performed using the AnnotaPipeline, resulting in a higher proportion of annotated proteins and a reduced proportion of hypothetical proteins when compared to the annotations publicly available for these organisms. AnnotaPipeline is a Unix-based pipeline developed using Python and is available at: https://github.com/bioinformatics-ufsc/AnnotaPipeline.
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Frechiani JPA, Matos PADSBA, Marcondes SS, Santos MDD, Araújo MP, Sipolatti ALRAC, Souza VB, Carrera WBM, Filho VB. RARA ASSOCIAÇÃO DE PÊNFIGO PARANEOPLÁSICO E BRONQUIOLITE OBLITERANTE EM PACIENTE COM DOENÇA DE CASTLEMAN UNICÊNTRICA: RELATO DE CASO. Hematol Transfus Cell Ther 2022. [DOI: 10.1016/j.htct.2022.09.128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Pires PGDS, Torres P, Teixeira Soratto TA, Filho VB, Hauptli L, Wagner G, Haese D, Pozzatti CD, Moraes PDO. Comparison of functional-oil blend and anticoccidial antibiotics effects on performance and microbiota of broiler chickens challenged by coccidiosis. PLoS One 2022; 17:e0270350. [PMID: 35793288 PMCID: PMC9258845 DOI: 10.1371/journal.pone.0270350] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 06/08/2022] [Indexed: 11/18/2022] Open
Abstract
This study aimed to compare the effects of different levels of cashew nutshell liquid (CNSL) and castor oil (CNSL-castor oil) with growth-promoting antibiotics associated with anticoccidials in broiler chickens challenged with coccidiosis. In this work, 2520 one-day-old male broiler chicks (Cobb) were randomly assigned to 84 pens, containing 30 birds each. The experimental design was completely randomized, with seven treatments: enramycin (8 ppm), virginiamycin (16.5 ppm), and tylosin (55 ppm); different doses of CNSL-castor oil (0.5, 0.75, and 1.00 kg/t); and a control diet (without additives). All treatments received semduramicin + nicarbazin (500 g/t; Aviax® Plus) from 0 to 28 d and monensin sodium (100 ppm; Elanco) from 29 to 35 days of age, when the feed was without antibiotics. The challenge was introduced at 14 days of age by inoculating broiler chickens with sporulated Eimeria tenella, Eimeria acervulina, and Eimeria maxima oocysts via oral gavage. In addition to performance parameters, intestinal contents were collected at 28 and 42 days of age for microbiota analysis by sequencing the 16s rRNA in V3 and V4 regions using the Illumina MiSeq platform. Taxonomy was assigned using the SILVA database (v. 138) with QIIME2 software (v. 2020.11). After one week of challenge, the broilers that received tylosin had a higher body weight gain (BWG) than those in the control group (p < 0.05), while the other treatments presented intermediate values. At 28 d, the BWG was lower for the control, CNSL-Castor oil 0.5 kg/t, enramycin, and virginiamycin treatments than that in the tylosin treatment. The inclusion of CNSL-Castor oil at concentrations of 0.75 and 1 kg/t acted as an intermediate treatment (p < 0.05). For alpha diversity, using the Shannon index, it was possible to observe the effect of age, with substantial diversity at 42 d. The Firmicutes phylum had the highest abundance, with values between 84.33% and 95.16% at 42 d. Tylosin showed better performance indices than other treatments. CNSL-castor oil treatments with concentrations of 0.75 and 1 kg/t showed similar results to those of enramycin and virginiamycin. Furthermore, CNSL-castor oil acted as a modulator of intestinal microbiota, reducing the abundance of pathogenic bacteria.
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Affiliation(s)
| | - Pedro Torres
- Department of Animal Science and Rural Development, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Tatiany Aparecida Teixeira Soratto
- Laboratory of Bioinformatics, Center of Biological Sciences, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Vilmar Benetti Filho
- Laboratory of Bioinformatics, Center of Biological Sciences, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Lucélia Hauptli
- Department of Animal Science and Rural Development, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Glauber Wagner
- Laboratory of Bioinformatics, Center of Biological Sciences, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Douglas Haese
- Centro de Tecnologia Animal Ltda, Domingos Martins, ES, Brazil
| | | | - Priscila de Oliveira Moraes
- Advanced Poultry Gut Science, Florianópolis, Santa Catarina, Brazil
- Department of Animal Science and Rural Development, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
- * E-mail:
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Beltrame LC, Zamparette CP, Feltrin C, da Cunha CR, Coltro EP, Athayde GSDS, Filho VB, Tápparo DC, Monteiro J, Kich JD, Palmeiro JK, Wagner G, Fongaro G, Zárate-Bladés CR, Sincero TCM. Different Swine Production Systems Can Shape Slurry Resistome at Mechanism and Class Levels Based on Swine Manure Evaluation. Front Cell Infect Microbiol 2022; 12:879656. [PMID: 35860383 PMCID: PMC9289446 DOI: 10.3389/fcimb.2022.879656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 05/30/2022] [Indexed: 11/14/2022] Open
Abstract
Antimicrobial resistance is a major threat to public health. Antimicrobial use in animal husbandry is a major concern since it can favor an increase in antimicrobial resistance among farms. Herein, we aim to better understand and characterize the main resistome profiles in microbial communities found in pig farms. Sampling of swine manure was performed in two different timepoints (October 2019 and January 2020) in each of the 14 different swine farms, located in the mesoregion of Western Santa Catarina state in Brazil, a pole of swine product production of worldwide importance. Samples were divided into three groups: farms with the opened regimen and no usage of antimicrobials (F1; n = 10), farms with the closed regimen and usage of antimicrobials (F2; n = 16), and farms with the closed regimen and no usage of antimicrobials (F3; n = 2). The metagenomic evaluation was performed to obtain and identify genetic elements related to antimicrobial resistance using nanopore sequencing. We used ResistoXplorer software to perform composition, alpha and beta diversity, and clustering analysis. In addition, PCR reactions were performed to confirm the presence or absence of seven different beta-lactamase family genes and five phosphoethanolamine transferase gene variants clinically relevant. Our findings based on the identification of resistance genes at the mechanism level showed a prevalence of alteration of the drug target (72.3%) profile, followed by drug inactivation (17.5%) and drug efflux (10.1%). We identified predominantly aminoglycosides (45.3%), tetracyclines (15.9%), and multiclass (11,2%) resistance genes. PCoA analysis indicates differences between F1 and F2 profiles. F2 samples showed increased diversity when compared to the F1 group. In addition, herein we first report the identification of mcr-4 in a slurry sample (C1F1.1) in Santa Catarina State. In general, our findings reinforce that many factors on the practices of animal husbandry are involved in the resistome profile at the mechanism and class levels. Further studies to better understand microbiome and mobilome aspects of these elements are necessary to elucidate transmission pathways between different bacteria and environments.
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Affiliation(s)
- Lucas Cafferati Beltrame
- Laboratory of Immunoregulation, iREG, Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, Brazil
- Laboratory of Applied Molecular Microbiology, MIMA, Department of Clinical Analysis, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Caetana Paes Zamparette
- Laboratory of Applied Molecular Microbiology, MIMA, Department of Clinical Analysis, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Clarissa Feltrin
- Laboratory of Applied Molecular Microbiology, MIMA, Department of Clinical Analysis, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Caroline Ribeiro da Cunha
- Laboratory of Applied Molecular Microbiology, MIMA, Department of Clinical Analysis, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Elisa Pires Coltro
- Laboratory of Immunoregulation, iREG, Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Gabriel Saldanha da Silva Athayde
- Laboratory of Applied Molecular Microbiology, MIMA, Department of Clinical Analysis, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Vilmar Benetti Filho
- Laboratory of Bioinformatics, Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, Brazil
| | | | - Jamir Monteiro
- Faculty of Veterinary Medicine, University of Southern Santa Catarina, Tubarão, Brazil
| | | | - Jussara Kasuko Palmeiro
- Laboratory of Applied Molecular Microbiology, MIMA, Department of Clinical Analysis, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Glauber Wagner
- Laboratory of Bioinformatics, Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Gislaine Fongaro
- Laboratory of Applied Virology, LVA, Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Carlos Rodrigo Zárate-Bladés
- Laboratory of Immunoregulation, iREG, Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Thaís Cristine Marques Sincero
- Laboratory of Applied Molecular Microbiology, MIMA, Department of Clinical Analysis, Federal University of Santa Catarina, Florianópolis, Brazil
- *Correspondence: Thaís Cristine Marques Sincero,
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Moreira RS, Filho VB, Calomeno NA, Wagner G, Miletti LC. EpiBuilder: A Tool for Assembling, Searching, and Classifying B-Cell Epitopes. Bioinform Biol Insights 2022; 16:11779322221095221. [PMID: 35571557 PMCID: PMC9102138 DOI: 10.1177/11779322221095221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/29/2022] [Indexed: 11/16/2022] Open
Abstract
Epitopes are portions of a protein that are recognized by antibodies. These small amino acid sequences represent a significant breakthrough in a branch of bioinformatics called immunoinformatics. Various software are available for linear B-cell epitope (BCE) prediction such as ABCPred, SVMTrip, EpiDope, and EpitopeVec; a well-known BCE predictor is BepiPred-2.0. However, despite the prediction, there are several essential steps, such as epitope assembly, evaluation, and searching for epitopes in other proteomes. Here, we present EpiBuilder (https://epibuilder.sourceforge.io), a user friendly software that assists in epitope assembly, classifying and searching using input results of BepiPred-2.0. EpiBuilder generates several output results from these data and supports a proteome-wide processing approach. In addition, this software provides the following features: Chou & Fasman beta-turn prediction, Emini surface accessibility prediction, Karplus and Schulz flexibility prediction, Kolaskar and Tongaonkar antigenicity, Parker hydrophilicity prediction, N-glycosylation domains, and hydropathy. These information generate a unique topology for each epitope, visually demonstrating its characteristics. The software can search the entire epitope sequence in various FASTA files, and it allows to use BLASTP to identify epitopes that eventually have sequence variations. As an EpiBuilder application, we developed a epitope dataset from the protozoan Trypanosoma brucei gambiense, the gram-positive bacterium Clostridioides difficile, and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
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Affiliation(s)
- Renato Simões Moreira
- Laboratório de Hemoparasitas e Vetores, Departamento de Produção Animal e Alimentos, Centro de Ciências Agroveterinárias (CAV), Universidade do Estado de Santa Catarina (UDESC), Lages, Brazil
- Instituto Federal de Santa Catarina (IFSC), Lages, Brazil
| | - Vilmar Benetti Filho
- Laboratório de Bioinformática, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Nathália Anderson Calomeno
- Laboratório de Hemoparasitas e Vetores, Departamento de Produção Animal e Alimentos, Centro de Ciências Agroveterinárias (CAV), Universidade do Estado de Santa Catarina (UDESC), Lages, Brazil
| | - Glauber Wagner
- Laboratório de Bioinformática, Universidade Federal de Santa Catarina, Florianópolis, Brazil
- Glauber Wagner, Laboratório de Bioinformática, Universidade Federal de Santa Catarina, Campus João David Ferreira Lima, Setor F, Bloco A, Sala 318, Caixa postal 476, Trindade, Florianópolis 88040-970, SC, Brazil.
| | - Luiz Claudio Miletti
- Laboratório de Hemoparasitas e Vetores, Departamento de Produção Animal e Alimentos, Centro de Ciências Agroveterinárias (CAV), Universidade do Estado de Santa Catarina (UDESC), Lages, Brazil
- Luiz Claudio Miletti, Laboratório de Hemoparasitas e Vetores, Departamento de Produção Animal e Alimentos, Centro de Ciências Agroveterinárias (CAV), Universidade do Estado de Santa Catarina (UDESC), Av. Luiz de Camões, 2090 Bairro Conta Dinheiro, Lages 88520-000, SC, Brazil.
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Carvalho VHR, Sonsim GS, Marcondes SS, Matos PADSBA, Araujo MP, Santos MDD, Filho VB, Frechiani JPA, Sipolatti ALRAC. PÚPURA TROMBOCITOPÊNICA TROMBÓTICA (PTT) RECIDIVADA/REFRATÁRIA: EXPERIÊNCIA DO CENTRO UNIVERSITÁRIO EM VITÓRIA – ES. Hematol Transfus Cell Ther 2021. [DOI: 10.1016/j.htct.2021.10.413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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