Subcultured Mycobacterium tuberculosis isolates on different growth media are fully representative of bacteria within clinical samples - 30/05/19

Doi : 10.1016/j.tube.2019.05.001

Charlotte Genestet ^a,^b,^⁎ , Elisabeth Hodille ^a,^c, Emilie Westeel ^a,^b, Christophe Ginevra ^a,^c, Florence Ader ^d, Samuel Venner ^e, Gérard Lina ^a,^c, Juliet E. Bryant ^a,^b, Jean-Luc Berland ^a,^b,^{^{1
JLB and OD contributed equally to this work.}}, Oana Dumitrescu ^a,^c,^{^{1
JLB and OD contributed equally to this work.}}
on behalf of the
Lyon TB study group
^a Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, Université de Lyon, Lyon, France
^b Fondation Mérieux, Lyon, France
^c Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de Bactériologie, Lyon, France
^d Service des Maladies Infectieuses et Tropicales, Hôpital de la Croix Rousse, Hospices Civils de Lyon, Lyon, France
^e Laboratoire de Biométrie et Biologie Evolutive (LBBE), CNRS UMR 5558, Université Lyon 1, Villeurbanne, France

^∗Corresponding author. Centre International de Recherche en Infectiologie, Université Lyon 1, ENS de Lyon, 21 Avenue Tony Garnier, 69365 Lyon cedex 07, France.Centre International de Recherche en InfectiologieUniversité Lyon 1ENS de Lyon21 Avenue Tony GarnierLyon cedex 0769365France

Abstract

Mycobacterium tuberculosis (Mtb) whole genome sequencing (WGS) plays an increasingly important role in tuberculosis diagnosis and research. WGS is typically performed on biobanked isolates obtained by subculture during diagnosis. Genetic variation upon culturing is known to occur in other bacterial species. However, little is understood regarding the impact of different subculture media on genome-wide diversity and variant selection in Mtb. Here we compared WGS derived from direct sequencing of sputa samples to WGS sequences from isolates subcultured on 3 different media. Based on analysis of single nucleotide polymorphisms (SNPs), there was no evidence of variant selection caused by the different culture media used, indicating that subcultured clinical strains can be reliably used to explore genetic determinants of Mtb pathogenesis and epidemiological features.

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Keywords : Mycobacterium tuberculosis, Whole genome sequencing, Virulence determinants, Genome-wide diversity