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Article: Comparative Genomic Analysis of Two Clonally Related Multidrug Resistant Mycobacterium tuberculosis by Single Molecule Real Time Sequencing

TitleComparative Genomic Analysis of Two Clonally Related Multidrug Resistant Mycobacterium tuberculosis by Single Molecule Real Time Sequencing
Authors
Keywordsmultidrug resistance
Mycobacterium tuberculosis
PacBio sequencing
growth rate
comparative genomic analysis
Issue Date2017
PublisherFrontiers Research Foundation. The Journal's web site is located at http://www.frontiersin.org/Cellular_and_Infection_Microbiology
Citation
Frontiers in Cellular and Infection Microbiology, 2017, v. 7, p. article no. 478 How to Cite?
AbstractBackground: Multidrug-resistant tuberculosis (MDR-TB) is posing a major threat to global TB control. In this study, we focused on two consecutive MDR-TB isolated from the same patient before and after the initiation of anti-TB treatment. To better understand the genomic characteristics of MDR-TB, Single Molecule Real-Time (SMRT) Sequencing and comparative genomic analyses was performed to identify mutations that contributed to the stepwise development of drug resistance and growth fitness in MDR-TB under in vivo challenge of anti-TB drugs. Result: Both pre-treatment and post-treatment strain demonstrated concordant phenotypic and genotypic susceptibility profiles toward rifampicin, pyrazinamide, streptomycin, fluoroquinolones, aminoglycosides, cycloserine, ethionamide, and para-aminosalicylic acid. However, although both strains carried identical missense mutations at rpoB S531L, inhA C-15T, and embB M306V, MYCOTB Sensititre assay showed that the post-treatment strain had 16-, 8-, and 4-fold elevation in the minimum inhibitory concentrations (MICs) toward rifabutin, isoniazid, and ethambutol respectively. The results have indicated the presence of additional resistant-related mutations governing the stepwise development of MDR-TB. Further comparative genomic analyses have identified three additional polymorphisms between the clinical isolates. These include a single nucleotide deletion at nucleotide position 360 of rv0888 in pre-treatment strain, and a missense mutation at rv3303c (lpdA) V44I and a 6-bp inframe deletion at codon 67–68 in rv2071c (cobM) in the post-treatment strain. Multiple sequence alignment showed that these mutations were occurring at highly conserved regions among pathogenic mycobacteria. Using structural-based and sequence-based algorithms, we further predicted that the mutations potentially have deleterious effect on protein function. Conclusion: This is the first study that compared the full genomes of two clonally-related MDR-TB clinical isolates during the course of anti-TB treatment. Our work has demonstrated the robustness of SMRT Sequencing in identifying mutations among MDR-TB clinical isolates. Comparative genome analysis also suggested novel mutations at rv0888, lpdA, and cobM that might explain the difference in antibiotic resistance and growth pattern between the two MDR-TB strains.
Persistent Identifierhttp://hdl.handle.net/10722/285242
ISSN
2019 Impact Factor: 4.123
2015 SCImago Journal Rankings: 2.748
PubMed Central ID

 

DC FieldValueLanguage
dc.contributor.authorLEUNG, KSS-
dc.contributor.authorSIU, GKH-
dc.contributor.authorTAM, KKG-
dc.contributor.authorTo, SWC-
dc.contributor.authorRajwani, Rahim-
dc.contributor.authorHo, PL-
dc.contributor.authorWong, SSY-
dc.contributor.authorZhao, WW-
dc.contributor.authorMa, OCK-
dc.contributor.authorYam, WC-
dc.date.accessioned2020-08-18T03:51:36Z-
dc.date.available2020-08-18T03:51:36Z-
dc.date.issued2017-
dc.identifier.citationFrontiers in Cellular and Infection Microbiology, 2017, v. 7, p. article no. 478-
dc.identifier.issn2235-2988-
dc.identifier.urihttp://hdl.handle.net/10722/285242-
dc.description.abstractBackground: Multidrug-resistant tuberculosis (MDR-TB) is posing a major threat to global TB control. In this study, we focused on two consecutive MDR-TB isolated from the same patient before and after the initiation of anti-TB treatment. To better understand the genomic characteristics of MDR-TB, Single Molecule Real-Time (SMRT) Sequencing and comparative genomic analyses was performed to identify mutations that contributed to the stepwise development of drug resistance and growth fitness in MDR-TB under in vivo challenge of anti-TB drugs. Result: Both pre-treatment and post-treatment strain demonstrated concordant phenotypic and genotypic susceptibility profiles toward rifampicin, pyrazinamide, streptomycin, fluoroquinolones, aminoglycosides, cycloserine, ethionamide, and para-aminosalicylic acid. However, although both strains carried identical missense mutations at rpoB S531L, inhA C-15T, and embB M306V, MYCOTB Sensititre assay showed that the post-treatment strain had 16-, 8-, and 4-fold elevation in the minimum inhibitory concentrations (MICs) toward rifabutin, isoniazid, and ethambutol respectively. The results have indicated the presence of additional resistant-related mutations governing the stepwise development of MDR-TB. Further comparative genomic analyses have identified three additional polymorphisms between the clinical isolates. These include a single nucleotide deletion at nucleotide position 360 of rv0888 in pre-treatment strain, and a missense mutation at rv3303c (lpdA) V44I and a 6-bp inframe deletion at codon 67–68 in rv2071c (cobM) in the post-treatment strain. Multiple sequence alignment showed that these mutations were occurring at highly conserved regions among pathogenic mycobacteria. Using structural-based and sequence-based algorithms, we further predicted that the mutations potentially have deleterious effect on protein function. Conclusion: This is the first study that compared the full genomes of two clonally-related MDR-TB clinical isolates during the course of anti-TB treatment. Our work has demonstrated the robustness of SMRT Sequencing in identifying mutations among MDR-TB clinical isolates. Comparative genome analysis also suggested novel mutations at rv0888, lpdA, and cobM that might explain the difference in antibiotic resistance and growth pattern between the two MDR-TB strains.-
dc.languageeng-
dc.publisherFrontiers Research Foundation. The Journal's web site is located at http://www.frontiersin.org/Cellular_and_Infection_Microbiology-
dc.relation.ispartofFrontiers in Cellular and Infection Microbiology-
dc.rightsThis Document is Protected by copyright and was first published by Frontiers. All rights reserved. It is reproduced with permission.-
dc.rightsThis work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.-
dc.subjectmultidrug resistance-
dc.subjectMycobacterium tuberculosis-
dc.subjectPacBio sequencing-
dc.subjectgrowth rate-
dc.subjectcomparative genomic analysis-
dc.titleComparative Genomic Analysis of Two Clonally Related Multidrug Resistant Mycobacterium tuberculosis by Single Molecule Real Time Sequencing-
dc.typeArticle-
dc.identifier.emailHo, PL: plho@hku.hk-
dc.identifier.emailWong, SSY: samsonsy@hku.hk-
dc.identifier.emailYam, WC: wcyam@hku.hk-
dc.identifier.authorityHo, PL=rp00406-
dc.identifier.authorityWong, SSY=rp00395-
dc.identifier.authorityYam, WC=rp00313-
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.3389/fcimb.2017.00478-
dc.identifier.pmid29188195-
dc.identifier.pmcidPMC5694780-
dc.identifier.scopuseid_2-s2.0-85034844498-
dc.identifier.hkuros312828-
dc.identifier.volume7-
dc.identifier.spagearticle no. 478-
dc.identifier.epagearticle no. 478-
dc.publisher.placeSwitzerland-

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