Whole genome sequencing Mycobacterium tuberculosis directly from sputum identifies more genetic diversity than sequencing from culture.
Drug-resistant tuberculosis
Heteroresistance
Mycobacterium tuberculosis
Sputum
Whole genome sequencing
Within-patient diversity
Journal
BMC genomics
ISSN: 1471-2164
Titre abrégé: BMC Genomics
Pays: England
ID NLM: 100965258
Informations de publication
Date de publication:
20 May 2019
20 May 2019
Historique:
received:
03
10
2018
accepted:
07
05
2019
entrez:
22
5
2019
pubmed:
22
5
2019
medline:
30
8
2019
Statut:
epublish
Résumé
Repeated culture reduces within-sample Mycobacterium tuberculosis genetic diversity due to selection of clones suited to growth in culture and/or random loss of lineages, but it is not known to what extent omitting the culture step altogether alters genetic diversity. We compared M. tuberculosis whole genome sequences generated from 33 paired clinical samples using two methods. In one method DNA was extracted directly from sputum then enriched with custom-designed SureSelect (Agilent) oligonucleotide baits and in the other it was extracted from mycobacterial growth indicator tube (MGIT) culture. DNA directly sequenced from sputum showed significantly more within-sample diversity than that from MGIT culture (median 5.0 vs 4.5 heterozygous alleles per sample, p = 0.04). Resistance associated variants present as HAs occurred in four patients, and in two cases may provide a genotypic explanation for phenotypic resistance. Culture-free M. tuberculosis whole genome sequencing detects more within-sample diversity than a leading culture-based method and may allow detection of mycobacteria that are not actively replicating.
Sections du résumé
BACKGROUND
BACKGROUND
Repeated culture reduces within-sample Mycobacterium tuberculosis genetic diversity due to selection of clones suited to growth in culture and/or random loss of lineages, but it is not known to what extent omitting the culture step altogether alters genetic diversity. We compared M. tuberculosis whole genome sequences generated from 33 paired clinical samples using two methods. In one method DNA was extracted directly from sputum then enriched with custom-designed SureSelect (Agilent) oligonucleotide baits and in the other it was extracted from mycobacterial growth indicator tube (MGIT) culture.
RESULTS
RESULTS
DNA directly sequenced from sputum showed significantly more within-sample diversity than that from MGIT culture (median 5.0 vs 4.5 heterozygous alleles per sample, p = 0.04). Resistance associated variants present as HAs occurred in four patients, and in two cases may provide a genotypic explanation for phenotypic resistance.
CONCLUSIONS
CONCLUSIONS
Culture-free M. tuberculosis whole genome sequencing detects more within-sample diversity than a leading culture-based method and may allow detection of mycobacteria that are not actively replicating.
Identifiants
pubmed: 31109296
doi: 10.1186/s12864-019-5782-2
pii: 10.1186/s12864-019-5782-2
pmc: PMC6528373
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
389Subventions
Organisme : Wellcome Trust
ID : 203583/Z/16/Z
Pays : United Kingdom
Organisme : National Institute for Health Research
ID : BRC/176/III/JB/101350
Organisme : Wellcome Trust
Pays : United Kingdom
Organisme : Medical Research Council
ID : MR/P007597/1
Pays : United Kingdom
Organisme : Seventh Framework Programme
ID : 304875
Commentaires et corrections
Type : ErratumIn
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