University of Khartoum

Genetic Analysis and Molecular basis of Multidrug Resistant Profile Exhibited by Clinical Isolates of Pseudomonas aeruginosa

Genetic Analysis and Molecular basis of Multidrug Resistant Profile Exhibited by Clinical Isolates of Pseudomonas aeruginosa

Show full item record

Title: Genetic Analysis and Molecular basis of Multidrug Resistant Profile Exhibited by Clinical Isolates of Pseudomonas aeruginosa
Author: Babiker, Mohamed Abdelrahman Hussain
Abstract: Background: Pseudomonas aeruginosa is known to be associated with resistance to practically all known antibiotics and is particularly problematic. The emergence of P. aeruginosa strains that are multi-resistant to β-lactams, aminoglycosides and quinolones becomes a serious problem. In order to understand MDR mechanism of P.aeruginosa, comparative genomic analysis and genetic feature should be defined. Objectives: The aim of this study was to determine the genomic profile and molecular characterization of multidrug resistant P.aeruginosa. Materials and Methods: This is a cross-sectional descriptive laboratory based analytical study in which 385 pre-identified P.aeruginosa clinical isolates were obtained from different Sudanese states. The isolates were re-examined and confirmed by biochemical tests and 16s rRNA, then subjected to antimicrobial susceptibility testing using disc diffusion method. DNA of 17 isolates were extracted by guanidine chloride method, 16s rRNA gene was amplified and DNA sequenced. Phylogenetic tree was constructed with another isolates (n=18) collected from NCBI. DNA of selected MDR isolate was extracted and its whole genome was sequenced. By using different bioinformatics tools, Whole genome of MDR isolate was assembled, annotated, announced and strain typing was determined using multilocus sequence typing, then subjected to comparative genomic with susceptible strains. Results: Two hundred (51.9%) isolates were confirmed as P.aeruginosa. The rate of resistance was 77.89%, 25.13%, 21.61%, 18.09%.5.53% and 4.52% for piperacillin, gentamicin, ciprofloxacin, ceftazidime, meropenem, and Polymyxin B respectively. The range of co-resistance among tested isolates was 2.5% - 23.5%. Eighteen per cent (36) of the tested isolates exhibited a MDR phenotype. Sequenced 16s rRNA genes were deposited to NCBI and the accession numbers were obtained, phylogenetic tree revealed that the isolates of this study were not in one cluster. The sequence type of the MDR strain was 235 indicating that it is circulating worldwide. Comparative genomic of MDR strain with susceptible strains revealed that, the core genes were shared by the three genomes but there were accessory genes that were strain-specific, and MDR genome has low CG% which makes it more susceptible to horizontal gene transfer. Prophage sequence was detected in MDR genome. There was no resistant island in MDR genome. One plasmid was detected but surprisingly contains no resistant gene for antipseudomonal drugs, that means, these genes were interspersed in the chromosome. 67 resistant genes were detected in MDR genome, 19 of them were found only in MDR genome. 48 genes were efflux pumps. Novel deleterious point mutation in gyrA gene has been detected at position D87G which is a known position behind quinolone resistance. Conclusion: There was a high rate of resistance to the first line of treatment. There were variations between MDR and susceptible strains regarding genome size, C+G% and number of antimicrobial resistant genes. It is expected that the main mechanism of resistance was through efflux pump with predominance of RND family. The MDR phenotype correlates with the presence of the relevant genes in MDR genome. Attribution of resistance to a specific mechanism may be difficult when more than one mechanism is involved.
URI: http://khartoumspace.uofk.edu/123456789/27448


Files in this item

Files Size Format View

This item appears in the following Collection(s)

Show full item record

Share

Search DSpace


Browse

My Account