Publicação
Survey of genomic features putatively contributing for antimicrobial resistance in Neisseria gonorrhoeae
| Resumo: | Globally, the impact of gonorrhea and antimicrobial resistance (AMR) in Neisseria gonorrhoeae are major public health concerns. This master's dissertation aimed to analyze the genetic diversity and AMR markers of N. gonorrhoeae strains circulating in Portugal between 1983 and 2022. First, AMR trends were evaluated from two collections of N. gonorrhoeae strains from a national network of laboratories, known as the "Legacy Collection" (n= 714) and PTGONONET (n= 5339). Within this dataset, it was observed that 46% of the strains showed resistance to ciprofloxacin, and from 2020 onwards, there was a significant increase in resistance to azithromycin until 2022. An analysis of trends in the circulation of genogroups over time was conducted, investigating the relative frequency of the ten most prevalent genogroups in Portugal from 1983 to 2022. The results revealed fluctuations in the genogroups over this period. The integration of the N. gonorrhoeae genomes from Portugal into a public European dataset allowed a detailed analysis of genetic diversity and genogroup circulation, revealing that the genogroups G002.001 and G001.002 not only predominate in Portugal but also in other parts of Europe. The second achieved objective was the development of an efficient technique to capture AMR markers directly from clinical samples through the application of an NGS amplicon-based scheme. This methodology was then applied to a set of 367 clinical samples and proved efficient in amplifying the target genes. Despite the reduced amplification rates observed in the folP and 23S rRNA genes, the overall amplification rate of the genes was high, around 84%. An in silico analysis was performed on clinical samples from different anatomical sites to identify antimicrobial resistance profiles. It was observed that more than 50% of the samples from all anatomical sites showed resistance or intermediate susceptibility to tetracycline, azithromycin, and ciprofloxacin. About cephalosporins, molecular data indicated a potentially reduced susceptibility. This study provided a detailed analysis of the evolution of antimicrobial resistance in N. gonorrhoeae in Portugal over nearly four decades. This historical analysis is essential for understanding the development of antibiotic resistance. One of the most innovative aspects of this dissertation is the implementation and validation of an NGS amplicon-based methodology. |
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| Autores principais: | Fonseca, Carolina Maria Moreira da |
| Assunto: | Neisseria gonorrhoeae Antimicrobial resistance Public health Genogroups Portugal Next Generation Sequencing |
| Ano: | 2024 |
| País: | Portugal |
| Tipo de documento: | dissertação de mestrado |
| Tipo de acesso: | acesso embargado |
| Instituição associada: | Universidade Nova de Lisboa |
| Idioma: | inglês |
| Origem: | Repositório Institucional da UNL |
| Resumo: | Globally, the impact of gonorrhea and antimicrobial resistance (AMR) in Neisseria gonorrhoeae are major public health concerns. This master's dissertation aimed to analyze the genetic diversity and AMR markers of N. gonorrhoeae strains circulating in Portugal between 1983 and 2022. First, AMR trends were evaluated from two collections of N. gonorrhoeae strains from a national network of laboratories, known as the "Legacy Collection" (n= 714) and PTGONONET (n= 5339). Within this dataset, it was observed that 46% of the strains showed resistance to ciprofloxacin, and from 2020 onwards, there was a significant increase in resistance to azithromycin until 2022. An analysis of trends in the circulation of genogroups over time was conducted, investigating the relative frequency of the ten most prevalent genogroups in Portugal from 1983 to 2022. The results revealed fluctuations in the genogroups over this period. The integration of the N. gonorrhoeae genomes from Portugal into a public European dataset allowed a detailed analysis of genetic diversity and genogroup circulation, revealing that the genogroups G002.001 and G001.002 not only predominate in Portugal but also in other parts of Europe. The second achieved objective was the development of an efficient technique to capture AMR markers directly from clinical samples through the application of an NGS amplicon-based scheme. This methodology was then applied to a set of 367 clinical samples and proved efficient in amplifying the target genes. Despite the reduced amplification rates observed in the folP and 23S rRNA genes, the overall amplification rate of the genes was high, around 84%. An in silico analysis was performed on clinical samples from different anatomical sites to identify antimicrobial resistance profiles. It was observed that more than 50% of the samples from all anatomical sites showed resistance or intermediate susceptibility to tetracycline, azithromycin, and ciprofloxacin. About cephalosporins, molecular data indicated a potentially reduced susceptibility. This study provided a detailed analysis of the evolution of antimicrobial resistance in N. gonorrhoeae in Portugal over nearly four decades. This historical analysis is essential for understanding the development of antibiotic resistance. One of the most innovative aspects of this dissertation is the implementation and validation of an NGS amplicon-based methodology. |
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