Project

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Name of Applicant : RIM GHARBI
Date of application : 13-10-2017
Unit : Integrated Mycobacterial Pathogenomics
Location : Guerin building-3st Floor
Phone : 0619406242
@ Mail : rim.gharbi@pasteur.fr
@ PI-Mail : roland.brosch@pasteur.fr

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Project context and summary :

In recent years, the number of non-tuberculous mycobacteria (NTM) isolated from clinical specimens has increased greatly, due to opportunistic infections accompanying immunosuppression, but also as a result of improved culture and identification techniques. It becomes increasingly clear that NTM, or at least some of them, might be responsible for difficult-to-treat infections in immunocompetent hosts. In this respect, we have undertaken a study aimed at characterizing NTM that were isolated from Tunisian patients suspected of pulmonary tuberculosis. For this purpose, we first studied the cultural and biochemical characteristics, as well as the drug susceptibility pattern, of NTM clinical strains. Next, we examined the polymorphism of three housekeeping genes, hsp65, rpoB, sodA, as well as 16S rRNA gene sequence. These genes were previously proposed in numerous independent studies as suitable phylogenetic markers for the classification of mycobacteria. In so doing, we have been able to properly classify the majority of NTM, while three isolates remained unassigned because of conflicting results in their phylogenetic signals based on the 4 sequenced genes. Hence, to unambiguously characterize and classify these NTM, we propose to sequence their whole genome, inasmuch as one isolate in particular showed unusual chromogenic features. The de novo sequencing was done at the Biomics platform of the Institut Pasteur, Paris using HiSeq 2500 technology (Illumina) with paired-end application. Automated cluster generation and paired end sequencing with dual index reads were performed in a single run in 2X107-pb, which will be the subject of a de novo assembly workflow and, in collaboration with the bioinformatic platform “C3BI” , the draft genome obtained will be functionally annotated and analysed with the Prokka program.

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