Banca de QUALIFICAÇÃO: Felipe Marques de Almeida

Uma banca de QUALIFICAÇÃO de DOUTORADO foi cadastrada pelo programa.
STUDENT : Felipe Marques de Almeida
DATE: 09/02/2024
TIME: 14:00
LOCAL: Videoconferência
TITLE:

"Development of scalable bioinformatics pipelines for comprehensive bacterial genomics analyses and application on a retrospective comparative study of multidrug resistance isolates from Brasilia."

KEY WORDS:

genomics; multidrug-resistance; antibiotics; klebsiella; pipelines; bioinformatics

PAGES: 1
BIG AREA: Ciências Biológicas
AREA: Biologia Geral
SUMMARY:

The advances in DNA sequencing technologies have reshaped bacterial genomics enabling chromosome-level assemblies at a fraction of cost and time. However, the full realization of this potential relies on computational resources to analyze the data. For this purpose, we have developed three efficient and standardized computer pipelines that comprehend the quality control of raw sequencing data, genome assembly, and extensive gene annotation with graphical reports. In particular, we provide an annotation module specialized for bacteria involved in nosocomial infections, which identifies antibiotic resistance genes (ARG), virulence factors, prophages, and integrative elements. To demonstrate their use, we sequenced and analyzed three Klebsiella pneumoniae samples from the University Hospital of Brasilia. The annotation revealed that they belong to the worldwide threat sequence type, ST 11, one of the major carbapenem-resistant Klebsiella pneumoniae (CRKP) lineages. We detected the presence of NDM-1, CTX-M-15, and OXA beta-lactamases genes in all three isolates, as well as several other ARGs distributed among chromosomes and plasmids. Additionally, virulence genes frequently related to hypervirulent strains, such as Salmochelin, have also been detected. Synteny analyses showed that besides the highly similar genome content, their genomes are structurally different, with several rearrangements observed. Finally, we carried out a retrospective comparative genomics analysis using other CRKP lineages isolated from Brasilia and other Brazilian locations. The results indicate that the resistance phenotype is shifting, with recent isolates displaying co-existence of multiple carbapenemases and other ARGs in their genomes. In conclusion, the results reiterate alerts about the emergence of high-risk clones due the convergence of resistance and virulence genes, reinforcing the need for pathogen surveillance programs for combating the spread of such high-risk characteristics.

COMMITTEE MEMBERS:
Externa ao Programa - 1357716 - BRUNA FUGA ARAUJO - nullPresidente - 1556610 - GEORGIOS JOANNIS PAPPAS JUNIOR
Externo ao Programa - 1421195 - LUIS CARLOS GUIMARAES - nullInterno - 1661623 - RICARDO HENRIQUE KRUGER
Externo ao Programa - 1876284 - VICENTE DE PAULO MARTINS - null