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COMPARATIVE GENOMIC ANALYSIS OF FOUR MOROCCAN CLINICAL STRAINS OF KLEBSIELLA PNEUMONIAE DISPLAYING DIFFERENT ANTIBIOTIC RESISTANCE PROFILES / Zineb KABBAJ 

Public ISBD Titre : COMPARATIVE GENOMIC ANALYSIS OF FOUR MOROCCAN CLINICAL STRAINS OF KLEBSIELLA PNEUMONIAE DISPLAYING DIFFERENT ANTIBIOTIC RESISTANCE PROFILES Type de document : thèse Auteurs : Zineb KABBAJ, Auteur Année de publication : 2020 Langues : Anglais (eng) Mots-clés : Klebsiella pneumoniae  outbreak  comparative genomic  antimicrobial resistance  MLST  Plasmids  Pan-genome  Klebsiella pneumoniae  épidémie  génomique comparative  résistance aux antimicrobiens  MLST  Plasmides  Pan-génome Résumé : Klebsiella Pneumoniae is now recognized as a major threat to human health globally because of the emergence of multidrug-resistant strains associated with hospital outbreaks and hypervirulent strains associated with severe community-acquired infections. However, very little research work has been carried out concerning the sequencing of the complete genome of K. pneumoniae. The objective of this study is to carry out a genomic analysis of four strains of K. Pneumoniae with different AMR profiles from different Moroccan patients in order to identify the resistance genes and perform a genomic comparison. Four strains of K. Pneumoniae were subjects of a de Novo assembly followed by an annotation in order to identify the genetic elements (resistance genes, plasmids...) of the strains. This genomic analysis pipeline made it possible to identify 31 resistance genes from different antimicrobial classes (β-lactam, aminoglycosides, Fosfomycin, fluoroquinolone…), 8 plasmids of different types (IncF, IncX, IncR, IncC, Col), 4 sequence types using MLST (ST664, ST13, ST2695, ST35) and a pan-genome of 4299 core genes and 1946 unique genes. Our study provided a global view of the information carried in the genome of K. Pneumoniae. There are multiple resistance genes across diverse Kp genomes and plasmids in circulation that are capable of carrying this resistance. Unless appropriate interventions are rapidly placed, these may lead to a massive problem of untreatable infection in vulnerable populations. Numéro (Thèse ou Mémoire) : MM0492020 Président : Azeddine IBRAHIMI Directeur : Tarek ALOUANE ; Latefa BISKRI Juge : Mouna OUADGHIRI Juge : Souad KARTTI COMPARATIVE GENOMIC ANALYSIS OF FOUR MOROCCAN CLINICAL STRAINS OF KLEBSIELLA PNEUMONIAE DISPLAYING DIFFERENT ANTIBIOTIC RESISTANCE PROFILES [thèse] / Zineb KABBAJ, Auteur . - 2020. Langues : Anglais (eng) Mots-clés : Klebsiella pneumoniae  outbreak  comparative genomic  antimicrobial resistance  MLST  Plasmids  Pan-genome  Klebsiella pneumoniae  épidémie  génomique comparative  résistance aux antimicrobiens  MLST  Plasmides  Pan-génome Résumé : Klebsiella Pneumoniae is now recognized as a major threat to human health globally because of the emergence of multidrug-resistant strains associated with hospital outbreaks and hypervirulent strains associated with severe community-acquired infections. However, very little research work has been carried out concerning the sequencing of the complete genome of K. pneumoniae. The objective of this study is to carry out a genomic analysis of four strains of K. Pneumoniae with different AMR profiles from different Moroccan patients in order to identify the resistance genes and perform a genomic comparison. Four strains of K. Pneumoniae were subjects of a de Novo assembly followed by an annotation in order to identify the genetic elements (resistance genes, plasmids...) of the strains. This genomic analysis pipeline made it possible to identify 31 resistance genes from different antimicrobial classes (β-lactam, aminoglycosides, Fosfomycin, fluoroquinolone…), 8 plasmids of different types (IncF, IncX, IncR, IncC, Col), 4 sequence types using MLST (ST664, ST13, ST2695, ST35) and a pan-genome of 4299 core genes and 1946 unique genes. Our study provided a global view of the information carried in the genome of K. Pneumoniae. There are multiple resistance genes across diverse Kp genomes and plasmids in circulation that are capable of carrying this resistance. Unless appropriate interventions are rapidly placed, these may lead to a massive problem of untreatable infection in vulnerable populations. Numéro (Thèse ou Mémoire) : MM0492020 Président : Azeddine IBRAHIMI Directeur : Tarek ALOUANE ; Latefa BISKRI Juge : Mouna OUADGHIRI Juge : Souad KARTTI

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GENOMIC ANALYSIS OF TWO BACILLUS STRAINS: BACILLUS VELEZENSIS QA2 AND BACILLUS LICHENIFORMIS QA1, AND IDENTIFICATION OF POTENTIAL GENES INVOLVED IN PHOSPHORUS SOLUBILIZATION / EZZAHIDI OUMAIMA

Public ISBD Titre : GENOMIC ANALYSIS OF TWO BACILLUS STRAINS: BACILLUS VELEZENSIS QA2 AND BACILLUS LICHENIFORMIS QA1, AND IDENTIFICATION OF POTENTIAL GENES INVOLVED IN PHOSPHORUS SOLUBILIZATION Type de document : thèse Auteurs : EZZAHIDI OUMAIMA, Auteur Année de publication : 2024 Langues : Anglais (eng) Mots-clés : Phosphorus  Comparative genomics  Bacillus licheniformis  Bacillus velezensis  WGS  Phosphore  Génomique comparative  Bacillus licheniformis  Bacillus velezensis  WGS  الفوسفور  الجينوميات المقارنة  باسيلوس ليشنيفورميس  باسيلوس فيليزينس  التسلسل الجينومي الكامل Résumé : Phosphorus, essential for agricultural productivity, is often inaccessible to plants due to its insoluble forms in soil. To address this challenge, our research undertakes a detailed genomic characterization of Bacillus velezensis QA2 and Bacillus licheniformis QA1. Known for their plant growth-promoting rhizobacteria (PGPR) traits, these strains are promising candidates for developing eco-friendly biofertilizers capable of effective phosphate solubilization. Using advanced high-throughput whole genome and Sanger sequencing technologies, we compared the genetic structures of B. velezensis QA2 and B. licheniformis QA1 to uncover specific genetic mechanisms that facilitate phosphate mobilization. Our discoveries reveal a complex network of genes responsible for the production of organic acids and phosphatases, which play important roles in transforming insoluble phosphates into forms accessible to plants. This genetic framework enhances our understanding of B. velezensis QA2's role in promoting plant growth and its potential to reduce dependence on chemical fertilizers. This genomic exploration significantly enriches our understanding of microbial capabilities in soil nutrient dynamics, highlighting the potential of microbial genomics in advancing sustainable agricultural technologies. By elucidating the molecular mechanisms through which these bacteria enhance soil fertility, the study lays the groundwork for targeted genetic enhancements and the strategic application of Bacillus strains in agriculture. These insights position B. velezensis QA2 and B. licheniformis QA1 as a key component in the future of biofertilizer technology, transforming agricultural practices towards sustainability. Numéro (Thèse ou Mémoire) : MM0232024 Président : OUADGHIRI Mouna Directeur : Joann Karen WHALEN, Um6p ; ERRAFII Khaoula, Um6p (AGC Juge : KANDOUSSI Ilham Juge : AANNIZ Tarik GENOMIC ANALYSIS OF TWO BACILLUS STRAINS: BACILLUS VELEZENSIS QA2 AND BACILLUS LICHENIFORMIS QA1, AND IDENTIFICATION OF POTENTIAL GENES INVOLVED IN PHOSPHORUS SOLUBILIZATION [thèse] / EZZAHIDI OUMAIMA, Auteur . - 2024. Langues : Anglais (eng) Mots-clés : Phosphorus  Comparative genomics  Bacillus licheniformis  Bacillus velezensis  WGS  Phosphore  Génomique comparative  Bacillus licheniformis  Bacillus velezensis  WGS  الفوسفور  الجينوميات المقارنة  باسيلوس ليشنيفورميس  باسيلوس فيليزينس  التسلسل الجينومي الكامل Résumé : Phosphorus, essential for agricultural productivity, is often inaccessible to plants due to its insoluble forms in soil. To address this challenge, our research undertakes a detailed genomic characterization of Bacillus velezensis QA2 and Bacillus licheniformis QA1. Known for their plant growth-promoting rhizobacteria (PGPR) traits, these strains are promising candidates for developing eco-friendly biofertilizers capable of effective phosphate solubilization. Using advanced high-throughput whole genome and Sanger sequencing technologies, we compared the genetic structures of B. velezensis QA2 and B. licheniformis QA1 to uncover specific genetic mechanisms that facilitate phosphate mobilization. Our discoveries reveal a complex network of genes responsible for the production of organic acids and phosphatases, which play important roles in transforming insoluble phosphates into forms accessible to plants. This genetic framework enhances our understanding of B. velezensis QA2's role in promoting plant growth and its potential to reduce dependence on chemical fertilizers. This genomic exploration significantly enriches our understanding of microbial capabilities in soil nutrient dynamics, highlighting the potential of microbial genomics in advancing sustainable agricultural technologies. By elucidating the molecular mechanisms through which these bacteria enhance soil fertility, the study lays the groundwork for targeted genetic enhancements and the strategic application of Bacillus strains in agriculture. These insights position B. velezensis QA2 and B. licheniformis QA1 as a key component in the future of biofertilizer technology, transforming agricultural practices towards sustainability. Numéro (Thèse ou Mémoire) : MM0232024 Président : OUADGHIRI Mouna Directeur : Joann Karen WHALEN, Um6p ; ERRAFII Khaoula, Um6p (AGC Juge : KANDOUSSI Ilham Juge : AANNIZ Tarik

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