Automated IS6110-based fingerprinting of Mycobacterium tuberculosis : reaching unprecedented discriminatory power and versatility

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dc.contributor.authorDekhil, Nairaen_ZA
dc.contributor.authorSkhairia, Mohamed Amineen_ZA
dc.contributor.authorMhenni, Besmaen_ZA
dc.contributor.authorFradj, Saloua Benen_ZA
dc.contributor.authorWarren, Roben_ZA
dc.contributor.authorMardassi, Helmien_ZA
dc.date.accessioned2020-05-25T14:02:44Z
dc.date.available2020-05-25T14:02:44Z
dc.date.issued2018
dc.descriptionCITATION: Dekhil, N., et al. 2018. Automated IS6110-based fingerprinting of Mycobacterium tuberculosis : reaching unprecedented discriminatory power and versatility. PLoS ONE, 13(6):e0197913, doi:10.1371/journal.pone.0197913.
dc.descriptionThe original publication is available at https://journals.plos.org/plosone/
dc.description.abstractBackground: Several technical hurdles and limitations have restricted the use of IS6110 restriction fragment length polymorphism (IS6110 RFLP), the most effective typing method for detecting recent tuberculosis (TB) transmission events. This has prompted us to conceive an alternative modality, IS6110-5’3’FP, a plasmid-based cloning approach coupled to a single PCR amplification of differentially labeled 5’ and 3’ IS6110 polymorphic ends and their automated fractionation on a capillary sequencer. The potential of IS6110-5’3’FP to be used as an alternative to IS6110 RFLP has been previously demonstrated, yet further technical improvements are still required for optimal discriminatory power and versatility. Objectives: Here we introduced critical amendments to the original IS6110-5’3’FP protocol and compared its performance to that of 24-loci multiple interspersed repetitive unit-variable number tandem repeats (MIRU-VNTR), the current standard method for TB transmission analyses. Methods: IS6110-5’3’FP protocol modifications involved: (i) the generation of smaller-sized polymorphic fragments for efficient cloning and PCR amplification, (ii) omission of the plasmid amplification step in E. coli for shorter turnaround times, (iii) the use of more stable fluorophores for increased sensitivity, (iv) automated subtraction of background fluorescent signals, and (v) the automated conversion of fluorescent peaks into binary data. Results: In doing so, the overall turnaround time of IS6110-5’3’FP was reduced to 4 hours. The new protocol allowed detecting almost all 5’ and 3’ IS6110 polymorphic fragments of any given strain, including IS6110 high-copy number Beijing strains. IS6110-5’3’FP proved much more discriminative than 24-loci MIRU-VNTR, particularly with strains of the M. tuberculosis lineage 4. Conclusions: The IS6110-5’3’FP protocol described herein reached the optimal discriminatory potential of IS6110 fingerprinting and proved more accurate than 24-loci MIRU-VNTR in estimating recent TB transmission. The method, which is highly cost-effective, was rendered versatile enough to prompt its evaluation as an automatized solution for a TB integrated molecular surveillance.en_ZA
dc.description.urihttps://journals.plos.org/plosone/article?id=10.1371/journal.pone.0197913
dc.description.versionPublisher's version
dc.format.extent15 pages
dc.identifier.citationDekhil, N., et al. 2018. Automated IS6110-based fingerprinting of Mycobacterium tuberculosis : reaching unprecedented discriminatory power and versatility. PLoS ONE, 13(6):e0197913, doi:10.1371/journal.pone.0197913
dc.identifier.issn1932-6203 (online)
dc.identifier.otherdoi:10.1371/journal.pone.0197913
dc.identifier.urihttp://hdl.handle.net/10019.1/108599
dc.language.isoen_ZAen_ZA
dc.publisherPublic Library of Science
dc.rights.holderAuthors retain copyright
dc.subjectMycobacterium tuberculosis -- Genetic aspecten_ZA
dc.subjectMycobacterium tuberculosis -- Transmissionen_ZA
dc.subjectDNA fingerprinting -- Automationen_ZA
dc.subjectRestriction enzymes, DNAen_ZA
dc.subjectNuclear fragmentationen_ZA
dc.subjectIS6110-5'3'FPen_ZA
dc.titleAutomated IS6110-based fingerprinting of Mycobacterium tuberculosis : reaching unprecedented discriminatory power and versatilityen_ZA
dc.typeArticleen_ZA
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