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Thèse de Doctorat
DOI
https://doi.org/10.11606/T.9.2023.tde-11032024-151818
Document
Auteur
Nom complet
Fernanda Ribeiro dos Santos Esposito
Adresse Mail
Unité de l'USP
Domain de Connaissance
Date de Soutenance
Editeur
São Paulo, 2023
Directeur
Jury
Lincopan, Nilton (Président)
Silva, André Pitondo da
Silva, Rodrigo Cayô da
Castillo, Danny Andrés Fuentes
Titre en anglais
Virulome and pathogenicity of multidrug-resistant World Health Organization priority pathogens
Mots-clés en anglais
Antimicrobial resistance
Galleria mellonella
One Health approach
Virulence
WGS
Resumé en anglais
The convergence of hypervirulence and resistance to carbapenems and to polymyxins in pathogens classified by the World Health Organization (WHO) as priority has been increasingly reported for human-animalenvironmental isolates around the world lately, thereby indicating a one health problem. As an integral part of the OneBR project (http://onehealthbr.com/), in the present study, 119 whole genomes of human, animal, environmental, and plant isolates of Escherichia coli (n=1), Klebsiella pneumoniae (n=101), and Pseudomonas aeruginosa (n=17)were sequenced with the aim of identifying the convergence between virulence and resistance. This dissertation is organized into six chapters, as follows: Chapter I Literature review and research justification Up-to-date literature review on pathogenicity, virulome, and convergence in the virulence and resistance of E. coli, K. pneumoniae, and P. aeruginosa isolates that are resistant to carbapenems and/or polymyxins. Chapter II Materials and methods Brief description of the materials and methods used in the research project. Chapter III - Genomic and phenotypic analyses of E. coli isolates Anexo 1 - Mucoviscosity induced by ciprofloxacin in CTX-M-15-producing Escherichia coli carrying the Klebsiella pneumoniae K23 gene cluster. Written article, in the process of finalizing corrections for submission to the International Journal of Antimicrobial Agents (Impact Factor 15.441), presenting for the first time the mucoviscosity phenotype induced by the presence of fluoroquinolones, chiefly ciprofloxacin, in a multiresistant strain of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli isolated from spinach leaves. Interestingly, the genomic analysis of this isolate detected virulence genes in charge of the synthesis of the K23 capsule were identified, confirming the presence of the phenotype observed previously. Moreover, by way of experiments with cells that resembled RAW macrophages, it was possible to identify a larger escape from phagocytosis by cells that had been previously exposed to ciprofloxacin, suggesting that the synthesized capsule is functional. Notably, this is the first report of fluoroquinolone-induced mucoviscosity phenotype in E. coli isolates, and identification of K23 serotype in E. coli isolates. Chapter IV Genomic and phenotypic analyses of K. pneumoniae isolates the K. pneumoniae genome bank, known as KpBR (http://onehealthbr.com/bacteria/KpBr), was developed so as to contribute to the epidemiological surveillance health systems in the management and control of antimicrobial resistance at the human-animal-environmental interface in Brazil. Appendix 2 - Genomic analysis of a Kpi (pilus system)-positive and CTX-M-15-producing Klebsiella pneumoniae belonging to the high-risk clone ST15 isolated from an impacted river in Brazil. Article published (https://doi.org/10.1016/j.ygeno.2021.12.007) in Genomics (Impact factor: 4.31, Qualis CAPES A2), in 2022. Appendix 3 - Successful expansion of healthcare-associated hypervirulent KPC-2- producing Klebsiella pneumoniae ST11/KL64 to impacted aquatic environment. Article published (https:// doi.org/10.1016/j.onehlt.2023.100594) in One Health Journal (Impact factor: 9.00), in 2023. Chapter V Genomic and phenotypic analysis of P. aeruginosa isolates The genome bank of P. aeruginosa, known as PaBr (http://onehealthbr.com/bacteria/PaBr), was developed to contribute to epidemiological surveillance health systems in the management and control of antimicrobial resistance at the human-animal- environmental interface in Brazil. Appendix 4 - Genomic analysis of carbapenem-resistant Pseudomonas aeruginosa isolated from urban rivers confirms spread of clone sequence type 277 carrying broad resistome and virulome beyond the hospital. Article published (https:// doi.org/10.3389/fmicb.2021.701921) in Frontiers in Microbiology (Impact factor: 6.064, Qualis CAPES A1), in 2021. Chapter VI Final remarks Major findings, contributions, and applications obtained from the present study.
Titre en portugais
Viruloma e patogenicidade de patógenos prioritários multirrresistentes listados pela Organização Mundial da Saúde
Mots-clés en portugais
Galleria mellonella
Resistência antimicrobiana
Saúde Única
Virulência
WGS
Resumé en portugais
A convergência de hipervirulência e resistência a carbapenêmicos e polimixinas em patógenos considerados prioritários pela Organização Mundial da Saúde (OMS), tem começado a ser reportado mundialmente em isolados de origem humana-animal-ambiental, o que constituí um problema de saúde única. Como parte do projeto OneBR (http://onehealthbr.com/), no presente estudo foram sequenciados um total de 119 genomas completos de isolados de Escherichia coli (n=1), Klebsiella pneumoniae (n=101) e Pseudomonas aeruginosa (n=17) de origem humana, animal, ambiental e vegetal, a fim de identificar o fenômeno da convergência de virulência e resistência. Esta tese foi subdividida em seis capítulos, conforme apresentado a seguir: Capítulo I - Revisão Bibliográfica e justificativa - Apresenta a revisão de literatura atualizada sobre a patogenicidade, viruloma e convergência de virulência e resistência de isolados de E. coli, K. pneumoniae e P. aeruginosa resistentes aos carbapenêmicos e/ou polimixinas. Capítulo II Materiais e métodos Descrição dos materiais e métodos utilizados no decorrer do projeto. Capítulo III - Análise genômica e fenotípica dos isolados de E. coli - Anexo 1 - Mucoviscosity induced by ciprofloxacin in CTX-M-15-producing Escherichia coli carrying the Klebsiella pneumoniae K23 gene cluster. Artigo submetido no periódico International Journal of Antimicrobial Agents (Fator de Impacto 15.441), apresentando pela primeira vez o fenótipo de mucoviscosidade induzida pela presença de fluoroquinolonas, principalmente a ciprofloxacina, em um isolado multirresistente de Escherichia coli produtor de β-lactamase de espectroestendido (ESBL), recuperado de folhas de espinafre. Interessantemente, realizando a análise do genoma deste isolado, genes de virulência responsáveis pela síntese de cápsula bacteriana pertencente ao sorotipo K23 foram identificados, corroborando o fenótipo observado anteriormente. Adicionalmente, através de experimentos realizados com célula semelhante a macrófagos do tipo RAW foi possível identificar maior evasão do sistema fagocitário por células previamente expostas à ciprofloxacina, sugerindo que cápsula sintetizada é funcional. Notavelmente, este se trata do primeiro relato de fenótipo de mucoviscosidade em isolados de E. coli induzido por fluoroquinolonas, bem como a identificação do sorotipo capsular K23 em isolados de E. coli. Capítulo IV - Análise genômica e fenotípica dos isolados de K. pneumoniae - O banco de dados genômicos de K. pneumoniae, denominado de KpBR (http://onehealthbr.com/bacteria/KpBr) foi desenvolvido, a fim de contribuir com os sistemas de saúde de vigilância epidemiológica, no gerenciamento e controle da resistência antimicrobiana na interface humana-animal-ambiental, no Brasil. Anexo 2 - Genomic analysis of a Kpi (pilus system)-positive and CTX-M-15-producing Klebsiella pneumoniae belonging to the high-risk clone ST15 isolated from an impacted river in Brazil. Artigo publicado (https://doi.org/10.1016/j.ygeno.2021.12.007) no periódico Genomics (Fator de Impacto 4.31, Qualis CAPES A2), em 2022. Anexo 3 - Expansion of healthcareassociated hypervirulent KPC-2-producing Klebsiella pneumoniae ST11/KL64 beyond hospital settings. Artigo publicado (https://doi.org/10.1016/j.onehlt.2023.100594) no periódico One Health Journal (Fator de Impacto 9.00, Qualis CAPES A1), em 2023. Capítulo V - Análise genômica e fenotípica dos isolados de P. aeruginosa - O banco de dados genômicos de P. aeruginosa, denominado de PaBr (http://onehealthbr.com/bacteria/PaBr) foi desenvolvido, a fim de contribuir com os sistemas de saúde de vigilância epidemiológica, no gerenciamento e controle da resistência antimicrobiana na interface humanaanimal-ambiental, no Brasil. Anexo 4 - Genomic analysis of carbapenem-resistant Pseudomonas aeruginosa isolated from urban rivers confirms spread of clone sequence type 277 carrying broad resistome and virulome beyond the hospital. Artigo publicado (https://doi.org/10.3389/fmicb.2021.701921) no periódico Frontiers in Microbiology (Fator de Impacto 6.064, Qualis CAPES A1), em 2021. Capítulo VI Considerações finais Principais resultados, contribuições e aplicações obtidas com o presente estudo.
 
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Date de Libération
2025-12-18
Date de Publication
2024-05-03
 
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