title: A proportion of mutations fixed in the genomes of in vitro selected isogenic drug-resistant Mycobacterium tuberculosis mutants can be detected as minority variants in the parent culture.
abstract: We studied genomic variation in a previously selected collection of isogenic Mycobacterium tuberculosis laboratory strains subjected to one or two rounds of antibiotic selection. Whole genome sequencing analysis identified eleven single, unique mutations (four synonymous, six non-synonymous, one intergenic), in addition to drug resistance-conferring mutations, that were fixed in the genomes of six monoresistant strains. Eight loci, present as minority variants (five non-synonymous, three synonymous) in the genome of the susceptible parent strain, became fixed in the genomes of multiple daughter strains. None of these mutations are known to be involved with drug resistance. Our results confirm previously observed genomic stability for M. tuberculosis, although the parent strain had accumulated allelic variants at multiple locations in an antibiotic-free in vitro environment. It is therefore likely to assume that these so-called hitchhiking mutations were co-selected and fixed in multiple daughter strains during antibiotic selection. The presence of multiple allelic variations, accumulated under non-selective conditions, which become fixed during subsequent selective steps, deserves attention. The wider availability of 'deep' sequencing methods could help to detect multiple bacterial (sub)populations within patients with high resolution and would therefore be useful in assisting in the detailed investigation of transmission chains.
authors: KIT Biomedical Research, Royal Tropical Institute, Meibergdreef 39, 1105 AZ Amsterdam, Netherlands i.bergval@kit.nl.
authors: Indra
authors: I
authors: Bergval
authors: London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom.
authors: Francesc
authors: F
authors: Coll
authors: KIT Biomedical Research, Royal Tropical Institute, Meibergdreef 39, 1105 AZ Amsterdam, Netherlands.
authors: Anja
authors: A
authors: Schuitema
authors: KIT Biomedical Research, Royal Tropical Institute, Meibergdreef 39, 1105 AZ Amsterdam, Netherlands.
authors: Hans
authors: H
authors: de Ronde
authors: London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom.
authors: Kim
authors: K
authors: Mallard
authors: King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia.
authors: Arnab
authors: A
authors: Pain
authors: London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom.
authors: Ruth
authors: R
authors: McNerney
authors: London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom.
authors: Taane G
authors: TG
authors: Clark
authors: KIT Biomedical Research, Royal Tropical Institute, Meibergdreef 39, 1105 AZ Amsterdam, Netherlands.
authors: Richard M
authors: RM
authors: Anthony
mesh_terms: D000483:Alleles; D000995:Antitubercular Agents / Q000494:pharmacology*; D024901:Drug Resistance, Multiple, Bacterial / Q000235:genetics*; D014644:Genetic Variation; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D009154:Mutation; D009169:Mycobacterium tuberculosis / Q000187:drug effects* / Q000235:genetics*; D010802:Phylogeny; D017422:Sequence Analysis, DNA
chemical_list: D000995:Antitubercular Agents
keywords: MDR-TB; drug resistance; evolution; mutation; tuberculosis; whole genome sequencing