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Affiner la recherche Faire une suggestionDEVELOPMENT OF GENOMICS TYPING WEBTOOL OF HELICOBACTER PYLORI / EL KAMILI FADOUA
Titre : DEVELOPMENT OF GENOMICS TYPING WEBTOOL OF HELICOBACTER PYLORI Type de document : thèse Auteurs : EL KAMILI FADOUA, Auteur Année de publication : 2022 Langues : Anglais (eng) Mots-clés : Helicobacter pylori website Drug resistance genomic Analysis Hélicobactere pylori Site Résistance aux antibiotics Analyse génomique هيليكوباكتر بيلوري موقع مقاومة المضادات الحيوية التحليل الجينومي Résumé : Helicobacter pylori is present in all regions of the world with a higher prevalence in developing countries. Almost half of the world’s population are infected with this bacterium. In this study, we present the first webtool for H pylori resistance, typing and virulence prediction based on the detection of SNPs and genes from WGS data of H pylori. The new webserver of H.pylori was made to make typing an easy approach by performing a detailed analysis of genetic variants of H.pylori strains, to provide information on genetic diversity and transmission of the bacteria in the whole world. The webserver also provides tools for virulence and resistance analysis which can play an important role in orienting the therapeutic approach and offer rapid identification and diagnosis for disease control and prevention. Numéro (Thèse ou Mémoire) : MM0232022 Président : Ibrahimi Azeddine Directeur : EL Allali Achraf Juge : Laamarti Mariem Juge : Kandoussi Ilham DEVELOPMENT OF GENOMICS TYPING WEBTOOL OF HELICOBACTER PYLORI [thèse] / EL KAMILI FADOUA, Auteur . - 2022.
Langues : Anglais (eng)
Mots-clés : Helicobacter pylori website Drug resistance genomic Analysis Hélicobactere pylori Site Résistance aux antibiotics Analyse génomique هيليكوباكتر بيلوري موقع مقاومة المضادات الحيوية التحليل الجينومي Résumé : Helicobacter pylori is present in all regions of the world with a higher prevalence in developing countries. Almost half of the world’s population are infected with this bacterium. In this study, we present the first webtool for H pylori resistance, typing and virulence prediction based on the detection of SNPs and genes from WGS data of H pylori. The new webserver of H.pylori was made to make typing an easy approach by performing a detailed analysis of genetic variants of H.pylori strains, to provide information on genetic diversity and transmission of the bacteria in the whole world. The webserver also provides tools for virulence and resistance analysis which can play an important role in orienting the therapeutic approach and offer rapid identification and diagnosis for disease control and prevention. Numéro (Thèse ou Mémoire) : MM0232022 Président : Ibrahimi Azeddine Directeur : EL Allali Achraf Juge : Laamarti Mariem Juge : Kandoussi Ilham Réservation
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Code barre Cote Support Localisation Section Disponibilité MM0232022 WA Thèse imprimé Unité des Thèses et Mémoires Mémoires de Masters Disponible Documents numériques
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Titre : MYCOBACTERIUM TUBERCULOSIS AND SARS-COV-2 GENOMIC ANALYSIS: INPUT INTO OUTBREAKS AND SURVEILLANCE INVESTIGATIONS Type de document : thèse Auteurs : Mariem LAAMARTI, Auteur Année de publication : 2021 Langues : Anglais (eng) Mots-clés : Mycobacterium Tuberculosis SARS-Cov-2 Genomic analysis Phylogeny drug resistance phylodynamic sequencing Mycobacterium Tuberculosis SARS-Cov-2 Analyse genomique Phylogenie resistance aux antibiotique , phylodynamique sequencage التحلیل الجینومي النشوء والتطور المقاومة الدینامیكا النباتیة SARS-CoV- المتفطرة السلیة 2 التسلسل Résumé : Comparative microbial genomics is increasingly used for high-resolution epidemiological
investigation of infectious agents' sources, transmission dynamics and antimicrobial
resistance.
In Chapter II, We performed the sequencing and genomic characterization of M.
Tuberculosis strains from Morocco to get insight into their genomic diversity, drug resistance,
population structure and identify potential mutations associated with drug resistance.
We conducted a whole-genome analysis of nine Morrocan M. tuberculosis isolates;
we identi ed 25 known mutations and 14 novel mutations in drug-associated genes and
provided experimental support for them. We found that all resistance and susceptible
strains clustered with LAM9 and Haarlem, respectively, belonging to the Euro-American
clade. The modelling of GyrA/GyrB mutations showed a decrease in the binding anity
with levo
oxacin.
Chapter III addresses the comparative genomic of SARS-CoV-2 from Morocco to
identify genetic variants as a crucial step in evaluating the spread in Morocco. This
study revealed 108 mutations in their genomes. The analysis haplotype network suggests
di erent sources of SARS-CoV-2 infection in Morocco.
In Chapter IV, we collected SARS-CoV-2 genomes isolated from 80 countries.The results
showed genotypes speci c to geographic location. Moreover, evolution over time has
demonstrated a mechanism of mutation co-accumulation, which might a ect the severity
and spread of the SARS-CoV-2 suggesting that a universal vaccine is more likely to be
ecient for all strains.
On the other hand, the selective pressure analysis revealed negatively selected residues
that could be considered therapeutic targets. We have also created an inclusive uni ed
database that lists all of the genetic variants of the SARS-CoV-2 genomes found in this
study.Numéro (Thèse ou Mémoire) : D0112021 Président : Abdallah BADOU Directeur : Azeddine IBRAHIMI ; Samir SIAH Juge : Rachid ELJAOUDI Juge : Laila SBABOU ; Mohammed EL AZAMI EL IDRISSI ; Juge : Lahcen BELYAMANI ; Mouna OUAD MYCOBACTERIUM TUBERCULOSIS AND SARS-COV-2 GENOMIC ANALYSIS: INPUT INTO OUTBREAKS AND SURVEILLANCE INVESTIGATIONS [thèse] / Mariem LAAMARTI, Auteur . - 2021.
Langues : Anglais (eng)
Mots-clés : Mycobacterium Tuberculosis SARS-Cov-2 Genomic analysis Phylogeny drug resistance phylodynamic sequencing Mycobacterium Tuberculosis SARS-Cov-2 Analyse genomique Phylogenie resistance aux antibiotique , phylodynamique sequencage التحلیل الجینومي النشوء والتطور المقاومة الدینامیكا النباتیة SARS-CoV- المتفطرة السلیة 2 التسلسل Résumé : Comparative microbial genomics is increasingly used for high-resolution epidemiological
investigation of infectious agents' sources, transmission dynamics and antimicrobial
resistance.
In Chapter II, We performed the sequencing and genomic characterization of M.
Tuberculosis strains from Morocco to get insight into their genomic diversity, drug resistance,
population structure and identify potential mutations associated with drug resistance.
We conducted a whole-genome analysis of nine Morrocan M. tuberculosis isolates;
we identi ed 25 known mutations and 14 novel mutations in drug-associated genes and
provided experimental support for them. We found that all resistance and susceptible
strains clustered with LAM9 and Haarlem, respectively, belonging to the Euro-American
clade. The modelling of GyrA/GyrB mutations showed a decrease in the binding anity
with levo
oxacin.
Chapter III addresses the comparative genomic of SARS-CoV-2 from Morocco to
identify genetic variants as a crucial step in evaluating the spread in Morocco. This
study revealed 108 mutations in their genomes. The analysis haplotype network suggests
di erent sources of SARS-CoV-2 infection in Morocco.
In Chapter IV, we collected SARS-CoV-2 genomes isolated from 80 countries.The results
showed genotypes speci c to geographic location. Moreover, evolution over time has
demonstrated a mechanism of mutation co-accumulation, which might a ect the severity
and spread of the SARS-CoV-2 suggesting that a universal vaccine is more likely to be
ecient for all strains.
On the other hand, the selective pressure analysis revealed negatively selected residues
that could be considered therapeutic targets. We have also created an inclusive uni ed
database that lists all of the genetic variants of the SARS-CoV-2 genomes found in this
study.Numéro (Thèse ou Mémoire) : D0112021 Président : Abdallah BADOU Directeur : Azeddine IBRAHIMI ; Samir SIAH Juge : Rachid ELJAOUDI Juge : Laila SBABOU ; Mohammed EL AZAMI EL IDRISSI ; Juge : Lahcen BELYAMANI ; Mouna OUAD Réservation
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Titre : SHOTGUN COMPARATIVE PROTEOMICS FOR IDENTIFICATION OF DRUG RESISTANCE SIGNATURES IN MYCOBACTERIUM TUBERCULOSIS ISOLATES Type de document : thèse Auteurs : ELHAOU FATIMA EZZAHRAA, Auteur Année de publication : 2023 Langues : Anglais (eng) Mots-clés : Tuberculosis Mycobacterium tuberculosis Comparative-proteomics Mass spectrometry Drug resistance Tuberculose Mycobacterium tuberculosis Protéomique-comparative Spectrométrie de masse Résistance aux antituberculeux السل المتفطرة السلية البروتينات المقارنة مطياف الكتلة مقاومة الأدوية Résumé : Tuberculosis (TB) is a persistent global health issue, especially due to the emergence of drug-resistant strains. Although TB rates have decreased worldwide, it remains a significant problem in certain regions like Morocco. In this study, we employed a Label-Free shotgun comparative proteomic approach to analyse protein expression differences between drugresistant and drug-sensitive Mycobacterium tuberculosis (MTB) isolates. To conduct the proteomic analysis, we used trypsin digestion in a bottom-up proteomic strategy to generate peptide fragments for further analysis. Ultra High-Performance Liquid Chromatography coupled with tandem mass spectrometry (LC-MS/MS) was utilized to separate and analyse these peptide fragments, enabling the identification and quantification of proteins in the drug-resistant and drug-sensitive MTB samples. By comparing the protein expression levels, we identified several proteins that were downregulated or upregulated in the multidrugresistant (MDR) samples compared to the drug-sensitive ones. Additionally, we quantified twenty proteins that were not expressed in the drug-sensitive samples and among these was the protein UPPP known to confer drug resistance to bacteria due its role in cell wall biosynthesis. Functional annotation and protein interaction networks were employed and elucidated the roles of these proteins in virulence and drug resistance mechanisms. Leveraging proteomic approaches to study the differential expression of these proteins holds great significance in exploring effective strategies for controlling drug resistance in Tuberculosis.
Numéro (Thèse ou Mémoire) : MM0202023 Président : OUADGHIRI Mouna Directeur : El ALLALI Achraf Juge : DAOUD Rachid Juge : BENTAYEBI Kaoutar SHOTGUN COMPARATIVE PROTEOMICS FOR IDENTIFICATION OF DRUG RESISTANCE SIGNATURES IN MYCOBACTERIUM TUBERCULOSIS ISOLATES [thèse] / ELHAOU FATIMA EZZAHRAA, Auteur . - 2023.
Langues : Anglais (eng)
Mots-clés : Tuberculosis Mycobacterium tuberculosis Comparative-proteomics Mass spectrometry Drug resistance Tuberculose Mycobacterium tuberculosis Protéomique-comparative Spectrométrie de masse Résistance aux antituberculeux السل المتفطرة السلية البروتينات المقارنة مطياف الكتلة مقاومة الأدوية Résumé : Tuberculosis (TB) is a persistent global health issue, especially due to the emergence of drug-resistant strains. Although TB rates have decreased worldwide, it remains a significant problem in certain regions like Morocco. In this study, we employed a Label-Free shotgun comparative proteomic approach to analyse protein expression differences between drugresistant and drug-sensitive Mycobacterium tuberculosis (MTB) isolates. To conduct the proteomic analysis, we used trypsin digestion in a bottom-up proteomic strategy to generate peptide fragments for further analysis. Ultra High-Performance Liquid Chromatography coupled with tandem mass spectrometry (LC-MS/MS) was utilized to separate and analyse these peptide fragments, enabling the identification and quantification of proteins in the drug-resistant and drug-sensitive MTB samples. By comparing the protein expression levels, we identified several proteins that were downregulated or upregulated in the multidrugresistant (MDR) samples compared to the drug-sensitive ones. Additionally, we quantified twenty proteins that were not expressed in the drug-sensitive samples and among these was the protein UPPP known to confer drug resistance to bacteria due its role in cell wall biosynthesis. Functional annotation and protein interaction networks were employed and elucidated the roles of these proteins in virulence and drug resistance mechanisms. Leveraging proteomic approaches to study the differential expression of these proteins holds great significance in exploring effective strategies for controlling drug resistance in Tuberculosis.
Numéro (Thèse ou Mémoire) : MM0202023 Président : OUADGHIRI Mouna Directeur : El ALLALI Achraf Juge : DAOUD Rachid Juge : BENTAYEBI Kaoutar Réservation
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