Avaliação de metodologia para análises in silico de dados de sequenciamento de genoma total de Klebsiella pneumoniae resistente a carbapenêmicos
Autor(a) principal: | |
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Data de Publicação: | 2021 |
Tipo de documento: | Dissertação |
Idioma: | por |
Título da fonte: | Manancial - Repositório Digital da UFSM |
Texto Completo: | http://repositorio.ufsm.br/handle/1/28340 |
Resumo: | The emergence of Klebsiella pneumoniae strains resistant to different antimicrobial classes has increased the concern regarding control and monitoring measures for this microorganism. Whole Genome Sequencing (WGS) has been used in epidemiological studies, public health investigations, as well as for tracking and monitoring outbreaks of multidrug-resistant pathogens. In addition, it allows the evaluation of multiple genes through online tools. The analysis and interpretation of data at a genomic scale is challenging due to the data volume, its complexity and the number of programs involved. The pipeline validation for WGS in clinical microbiology is still poorly described. Thus, the present study aimed to validate a bioinformatics pipeline for the antimicrobial resistance genes identification from carbapenemresistant Klebsiella pneumoniae WGS. Sequences were obtained from a publicly available database, trimmed, de novo assembled, mapped to the K. pneumoniae reference genome and annotated. Contigs were submitted to different databases for bacterial (Kraken 2 and SpeciesFinder) and antimicrobial resistance genes (ResFinder and ABRicate) identifications in order to produce standardized methodologies that allow interlaboratory comparisons. The pipeline performance evaluation was carried out according to traditional metrics of repeatability, reproducibility, accuracy, precision, sensitivity and specificity, adapted to the objective of the study. As a result, 100% repeatability and reproducibility were obtained for the evaluated databases. For the other performance metrics, 99.99% accuracy, 83.53% precision, 75.45% sensitivity and 100% specificity were obtained for the ResFinder database. For the ABRicate database, 99.99% accuracy, 83.78% precision, 75.18% sensitivity and 100% specificity were obtained. Discrepancies in bacterial identification and detection of resistance genes were observed probably due to the difference in databases. Due to the range of bioinformatics tools and databases, validation is of paramount importance. The validation strategy used in our study can be applied in different bioinformatics pipelines and databases to ensure intra and interlaboratory standardization. |
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Avaliação de metodologia para análises in silico de dados de sequenciamento de genoma total de Klebsiella pneumoniae resistente a carbapenêmicosEvaluation of methodology for in silico analyses of whole genome sequencing data from carbapenem resistant Klebsiella pneumoniaeK. pneumoniaeValidaçãoResistência aos antimicrobianosWhole genome sequencingValidationAntimicrobial resistanceCNPQ::CIENCIAS DA SAUDE::FARMACIAThe emergence of Klebsiella pneumoniae strains resistant to different antimicrobial classes has increased the concern regarding control and monitoring measures for this microorganism. Whole Genome Sequencing (WGS) has been used in epidemiological studies, public health investigations, as well as for tracking and monitoring outbreaks of multidrug-resistant pathogens. In addition, it allows the evaluation of multiple genes through online tools. The analysis and interpretation of data at a genomic scale is challenging due to the data volume, its complexity and the number of programs involved. The pipeline validation for WGS in clinical microbiology is still poorly described. Thus, the present study aimed to validate a bioinformatics pipeline for the antimicrobial resistance genes identification from carbapenemresistant Klebsiella pneumoniae WGS. Sequences were obtained from a publicly available database, trimmed, de novo assembled, mapped to the K. pneumoniae reference genome and annotated. Contigs were submitted to different databases for bacterial (Kraken 2 and SpeciesFinder) and antimicrobial resistance genes (ResFinder and ABRicate) identifications in order to produce standardized methodologies that allow interlaboratory comparisons. The pipeline performance evaluation was carried out according to traditional metrics of repeatability, reproducibility, accuracy, precision, sensitivity and specificity, adapted to the objective of the study. As a result, 100% repeatability and reproducibility were obtained for the evaluated databases. For the other performance metrics, 99.99% accuracy, 83.53% precision, 75.45% sensitivity and 100% specificity were obtained for the ResFinder database. For the ABRicate database, 99.99% accuracy, 83.78% precision, 75.18% sensitivity and 100% specificity were obtained. Discrepancies in bacterial identification and detection of resistance genes were observed probably due to the difference in databases. Due to the range of bioinformatics tools and databases, validation is of paramount importance. The validation strategy used in our study can be applied in different bioinformatics pipelines and databases to ensure intra and interlaboratory standardization.Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPESA emergência de cepas de Klebsiella pneumoniae resistentes a diversas classes de antimicrobianos tem aumentado a preocupação com medidas de controle e monitoramento deste microrganismo. O sequenciamento do genoma total (Whole Genome Sequencing – WGS) vem sendo utilizado em estudos epidemiológicos, investigações em saúde pública, para rastreamento e monitoramento de surtos de patógenos multirresistentes. Além disso, possibilita a avaliação de múltiplos genes através de ferramentas de bioinformática. A análise e interpretação de genomas é desafiadora devido ao grande volume de dados, sua complexidade e número de programas envolvidos. A validação de pipelines para WGS na microbiologia clínica ainda é pouco descrita. Desse modo, o presente estudo teve como objetivo validar um pipeline de bioinformática para identificação de genes de resistência aos antimicrobianos em sequências de genoma total de Klebsiella pneumoniae resistente aos carbapenêmicos. As sequências foram obtidas de uma base de dados de acesso público, trimadas, montadas de novo, mapeadas no genoma de referência de K. pneumoniae e anotadas. Os contigs foram submetidos a diferentes bancos de dados para identificação bacteriana (Kraken 2 e SpeciesFinder) e de genes de resistência aos antimicrobianos (ResFinder e ABRicate) com a finalidade de produzir metodologias padronizadas que permitam comparações interlaboratoriais. A avaliação de desempenho do pipeline foi realizada de acordo com métricas tradicionais de repetibilidade, reprodutibilidade, acurácia, precisão, sensibilidade e especificidade, adaptadas ao objetivo do estudo. Obteve-se como resultado 100% de repetibilidade e reprodutibilidade para os bancos de dados avaliados. Para as demais métricas de desempenho obteve-se 99,99% de acurácia, 83,53% de precisão, 75,45% de sensibilidade e 100% de especificidade para o banco de dados ResFinder. Para o banco de dados ABRicate obteve-se 99,99% de acurácia, 83,78% de precisão, 75,18% de sensibilidade e 100% de especificidade. Discrepâncias na identificação bacteriana e na detecção de genes de resistência foram observadas provavelmente pela diferença nos bancos de dados. Em virtude da gama de ferramentas de bioinformática e bancos de dados, a validação é de suma importância. A estratégia de validação utilizada em nosso estudo pode ser aplicada em diferentes pipelines de bioinformática e bancos de dados para garantir padronização intra e interlaboratoriais.Universidade Federal de Santa MariaBrasilFarmáciaUFSMPrograma de Pós-Graduação em Ciências FarmacêuticasCentro de Ciências da SaúdeTrindade, Priscila de Arrudahttp://lattes.cnpq.br/0124362929241308Côrtes, Marina FarrelMartins, Roberta Cristina RuedasVieira, Andressa de Almeida2023-03-23T11:32:22Z2023-03-23T11:32:22Z2021-10-14info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/masterThesisapplication/pdfhttp://repositorio.ufsm.br/handle/1/28340porAttribution-NonCommercial-NoDerivatives 4.0 Internationalhttp://creativecommons.org/licenses/by-nc-nd/4.0/info:eu-repo/semantics/openAccessreponame:Manancial - Repositório Digital da UFSMinstname:Universidade Federal de Santa Maria (UFSM)instacron:UFSM2023-03-23T11:32:22Zoai:repositorio.ufsm.br:1/28340Biblioteca Digital de Teses e Dissertaçõeshttps://repositorio.ufsm.br/ONGhttps://repositorio.ufsm.br/oai/requestatendimento.sib@ufsm.br||tedebc@gmail.comopendoar:2023-03-23T11:32:22Manancial - Repositório Digital da UFSM - Universidade Federal de Santa Maria (UFSM)false |
dc.title.none.fl_str_mv |
Avaliação de metodologia para análises in silico de dados de sequenciamento de genoma total de Klebsiella pneumoniae resistente a carbapenêmicos Evaluation of methodology for in silico analyses of whole genome sequencing data from carbapenem resistant Klebsiella pneumoniae |
title |
Avaliação de metodologia para análises in silico de dados de sequenciamento de genoma total de Klebsiella pneumoniae resistente a carbapenêmicos |
spellingShingle |
Avaliação de metodologia para análises in silico de dados de sequenciamento de genoma total de Klebsiella pneumoniae resistente a carbapenêmicos Vieira, Andressa de Almeida K. pneumoniae Validação Resistência aos antimicrobianos Whole genome sequencing Validation Antimicrobial resistance CNPQ::CIENCIAS DA SAUDE::FARMACIA |
title_short |
Avaliação de metodologia para análises in silico de dados de sequenciamento de genoma total de Klebsiella pneumoniae resistente a carbapenêmicos |
title_full |
Avaliação de metodologia para análises in silico de dados de sequenciamento de genoma total de Klebsiella pneumoniae resistente a carbapenêmicos |
title_fullStr |
Avaliação de metodologia para análises in silico de dados de sequenciamento de genoma total de Klebsiella pneumoniae resistente a carbapenêmicos |
title_full_unstemmed |
Avaliação de metodologia para análises in silico de dados de sequenciamento de genoma total de Klebsiella pneumoniae resistente a carbapenêmicos |
title_sort |
Avaliação de metodologia para análises in silico de dados de sequenciamento de genoma total de Klebsiella pneumoniae resistente a carbapenêmicos |
author |
Vieira, Andressa de Almeida |
author_facet |
Vieira, Andressa de Almeida |
author_role |
author |
dc.contributor.none.fl_str_mv |
Trindade, Priscila de Arruda http://lattes.cnpq.br/0124362929241308 Côrtes, Marina Farrel Martins, Roberta Cristina Ruedas |
dc.contributor.author.fl_str_mv |
Vieira, Andressa de Almeida |
dc.subject.por.fl_str_mv |
K. pneumoniae Validação Resistência aos antimicrobianos Whole genome sequencing Validation Antimicrobial resistance CNPQ::CIENCIAS DA SAUDE::FARMACIA |
topic |
K. pneumoniae Validação Resistência aos antimicrobianos Whole genome sequencing Validation Antimicrobial resistance CNPQ::CIENCIAS DA SAUDE::FARMACIA |
description |
The emergence of Klebsiella pneumoniae strains resistant to different antimicrobial classes has increased the concern regarding control and monitoring measures for this microorganism. Whole Genome Sequencing (WGS) has been used in epidemiological studies, public health investigations, as well as for tracking and monitoring outbreaks of multidrug-resistant pathogens. In addition, it allows the evaluation of multiple genes through online tools. The analysis and interpretation of data at a genomic scale is challenging due to the data volume, its complexity and the number of programs involved. The pipeline validation for WGS in clinical microbiology is still poorly described. Thus, the present study aimed to validate a bioinformatics pipeline for the antimicrobial resistance genes identification from carbapenemresistant Klebsiella pneumoniae WGS. Sequences were obtained from a publicly available database, trimmed, de novo assembled, mapped to the K. pneumoniae reference genome and annotated. Contigs were submitted to different databases for bacterial (Kraken 2 and SpeciesFinder) and antimicrobial resistance genes (ResFinder and ABRicate) identifications in order to produce standardized methodologies that allow interlaboratory comparisons. The pipeline performance evaluation was carried out according to traditional metrics of repeatability, reproducibility, accuracy, precision, sensitivity and specificity, adapted to the objective of the study. As a result, 100% repeatability and reproducibility were obtained for the evaluated databases. For the other performance metrics, 99.99% accuracy, 83.53% precision, 75.45% sensitivity and 100% specificity were obtained for the ResFinder database. For the ABRicate database, 99.99% accuracy, 83.78% precision, 75.18% sensitivity and 100% specificity were obtained. Discrepancies in bacterial identification and detection of resistance genes were observed probably due to the difference in databases. Due to the range of bioinformatics tools and databases, validation is of paramount importance. The validation strategy used in our study can be applied in different bioinformatics pipelines and databases to ensure intra and interlaboratory standardization. |
publishDate |
2021 |
dc.date.none.fl_str_mv |
2021-10-14 2023-03-23T11:32:22Z 2023-03-23T11:32:22Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/masterThesis |
format |
masterThesis |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://repositorio.ufsm.br/handle/1/28340 |
url |
http://repositorio.ufsm.br/handle/1/28340 |
dc.language.iso.fl_str_mv |
por |
language |
por |
dc.rights.driver.fl_str_mv |
Attribution-NonCommercial-NoDerivatives 4.0 International http://creativecommons.org/licenses/by-nc-nd/4.0/ info:eu-repo/semantics/openAccess |
rights_invalid_str_mv |
Attribution-NonCommercial-NoDerivatives 4.0 International http://creativecommons.org/licenses/by-nc-nd/4.0/ |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.publisher.none.fl_str_mv |
Universidade Federal de Santa Maria Brasil Farmácia UFSM Programa de Pós-Graduação em Ciências Farmacêuticas Centro de Ciências da Saúde |
publisher.none.fl_str_mv |
Universidade Federal de Santa Maria Brasil Farmácia UFSM Programa de Pós-Graduação em Ciências Farmacêuticas Centro de Ciências da Saúde |
dc.source.none.fl_str_mv |
reponame:Manancial - Repositório Digital da UFSM instname:Universidade Federal de Santa Maria (UFSM) instacron:UFSM |
instname_str |
Universidade Federal de Santa Maria (UFSM) |
instacron_str |
UFSM |
institution |
UFSM |
reponame_str |
Manancial - Repositório Digital da UFSM |
collection |
Manancial - Repositório Digital da UFSM |
repository.name.fl_str_mv |
Manancial - Repositório Digital da UFSM - Universidade Federal de Santa Maria (UFSM) |
repository.mail.fl_str_mv |
atendimento.sib@ufsm.br||tedebc@gmail.com |
_version_ |
1805922137851035648 |