Draft Genome Sequences of the Mycobacterium tuberculosis Clinical Strains A2 and A4, Isolated from a Relapse Patient in Taiwan

Liao, Yu-Chieh; Chen, Yih-Yuan; Lin, Hsin-Hung; Chang, Jinghua Tsai; Su, Ih‐Jen; Huang, Tsi-Shu; Dou, Horng-Yunn

doi:10.1128/genomea.00672-14

Cited by 3 publications

(2 citation statements)

References 9 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The first dataset comprised of 11 whole-genome-sequenced M. tuberculosis strains for which the experimental 24-loci MIRU-VNTR profiles have been described in previous publications ( Clemmensen et al, 2017 ; Ilina et al, 2013 ; Kotłowski, 2015 ; Liao et al, 2014 ; Mokrousov, 2013 ; Rodríguez-Castillo et al, 2017 ; Roetzer et al, 2013 ; Roetzer et al, 2011 ). These 11 strains were identified through a literature review as follows: (1) Searching over 6,000 published articles in the Genome Announcements (an American society for microbiology journal that publishes short descriptions on microbial genomes in the public databases) with keywords “Mycobacterium tuberculosis” AND “MIRU-VNTR”.…”

Section: Methodsmentioning

confidence: 99%

MIRU-profiler: a rapid tool for determination of 24-loci MIRU-VNTR profiles from assembled genomes ofMycobacterium tuberculosis

Rajwani

Shehzad

Siu

2018

PeerJ

View full text Add to dashboard Cite

BackgroundTuberculosis (TB) resulted in an estimated 1.7 million deaths in the year 2016. The disease is caused by the members of Mycobacterium tuberculosis complex, which includes Mycobacterium tuberculosis, Mycobacterium bovis and other closely related TB causing organisms. In order to understand the epidemiological dynamics of TB, national TB control programs often conduct standardized genotyping at 24 Mycobacterial-Interspersed-Repetitive-Units (MIRU)-Variable-Number-of-Tandem-Repeats (VNTR) loci. With the advent of next generation sequencing technology, whole-genome sequencing (WGS) has been widely used for studying TB transmission. However, an open-source software that can connect WGS and MIRU-VNTR typing is currently unavailable, which hinders interlaboratory communication. In this manuscript, we introduce the MIRU-profiler program which could be used for prediction of MIRU-VNTR profile from WGS of M. tuberculosis.ImplementationThe MIRU-profiler is implemented in shell scripting language and depends on EMBOSS software. The in-silico workflow of MIRU-profiler is similar to those described in the laboratory manuals for genotyping M. tuberculosis. Given an input genome sequence, the MIRU-profiler computes alleles at the standard 24-loci based on in-silico PCR amplicon lengths. The final output is a tab-delimited text file detailing the 24-loci MIRU-VNTR pattern of the input sequence.ValidationThe MIRU-profiler was validated on four datasets: complete genomes from NCBI-GenBank (n = 11), complete genomes for locally isolated strains sequenced using PacBio (n = 4), complete genomes for BCG vaccine strains (n = 2) and draft genomes based on 250 bp paired-end Illumina reads (n = 106).ResultsThe digital MIRU-VNTR results were identical to the experimental genotyping results for complete genomes of locally isolated strains, BCG vaccine strains and five out of 11 genomes from the NCBI-GenBank. For draft genomes based on short Illumina reads, 21 out of 24 loci were inferred with a high accuracy, while a number of inaccuracies were recorded for three specific loci (ETRA, QUB11b and QUB26). One of the unique features of the MIRU-profiler was its ability to process multiple genomes in a batch. This feature was tested on all complete M. tuberculosis genome (n = 157), for which results were successfully obtained in approximately 14 min.ConclusionThe MIRU-profiler is a rapid tool for inference of digital MIRU-VNTR profile from the assembled genome sequences. The tool can accurately infer repeat numbers at the standard 24 or 21/24 MIRU-VNTR loci from the complete or draft genomes respectively. Thus, the tool is expected to bridge the communication gap between the laboratories using WGS and those using the conventional MIRU-VNTR typing.

show abstract

Section: Methodsmentioning

confidence: 99%

MIRU-profiler: a rapid tool for determination of 24-loci MIRU-VNTR profiles from assembled genomes ofMycobacterium tuberculosis

Rajwani

Shehzad

Siu

2018

PeerJ

View full text Add to dashboard Cite

show abstract

“…[7][8][9][10] In the present study, six MTB strains − isolates of the Beijing ancient sublineage, the Beijing modern sublineage, Haarlem, EAI, T1, and Latin-American Mediterranean (LAM) − representing the major types of clinical strains isolated from three different ethnic groups (aboriginals, Han Chinese, "veterans") in Taiwan 7,8 were subjected to whole-genome sequencing. [11][12][13] The six Taiwan genomes were then compared to four reference MTB strains (H37Rv, H37Ra, CDC 1551 (LAM), and F11 (LAM) [14][15][16] ) as well as the genome of Mycobacterium bovis. The presence of significant sequence diversity in MTB could provide a basis for understanding pathogenesis, immune mechanisms, and bacterial evolution.…”

Section: Genomics Study Of Mycobacterium Tuberculosis Strains From Different Ethnic Populations In Taiwanmentioning

confidence: 99%

Genomics Study of Mycobacterium tuberculosis Strains from Different Ethnic Populations in Taiwan

Dou

Chen

et al. 2016

Evol Bioinform Online

Self Cite

View full text Add to dashboard Cite

To better understand the transmission and evolution of Mycobacterium tuberculosis (MTB) in Taiwan, six different MTB isolates (representatives of the Beijing ancient sublineage, Beijing modern sublineage, Haarlem, East-African Indian, T1, and Latin-American Mediterranean (LAM)) were characterized and their genomes were sequenced. Discriminating among large sequence polymorphisms (LSPs) that occur once versus those that occur repeatedly in a genomic region may help to elucidate the biological roles of LSPs and to identify the useful phylogenetic relationships. In contrast to our previous LSP-based phylogeny, the sequencing data allowed us to determine actual genetic distances and to define precisely the phylogenetic relationships between the main lineages of the MTB complex. Comparative genomics analyses revealed more nonsynonymous substitutions than synonymous changes in the coding sequences. Furthermore, MTB isolate M7, a LAM-3 clinical strain isolated from a patient of Taiwanese aboriginal origin, is closely related to F11 (LAM), an epidemic tuberculosis strain isolated in the Western Cape of South Africa. The PE/PPE protein family showed a higher dn/ds ratio compared to that for all protein-coding genes. Finally, we found Haarlem-3 and LAM-3 isolates to be circulating in the aboriginal community in Taiwan, suggesting that they may have originated with post-Columbus Europeans. Taken together, our results revealed an interesting association with historical migrations of different ethnic populations, thus providing a good model to explore the global evolution and spread of MTB.

show abstract

Lineage-specific SNPs for genotyping of Mycobacterium tuberculosis clinical isolates

Dou

Lin

Chen

et al. 2017

Sci Rep

Self Cite

View full text Add to dashboard Cite

Tuberculosis (TB) is a severe infectious disease worldwide. Genetic variation of the causative agent, Mycobacterium tuberculosis (MTB), determines the outcomes of infection and anti-TB treatment. Until recently, there has been no effective and convenient way for classifying clinical isolates based on the DNA sequences of the divergent lineages of MTB infecting human populations. Here, we identified single nucleotide polymorphisms (SNPs) of six representative strains from Taiwan by whole-genome sequencing and comparing the results to the sequence of the H37Rv reference strain. One hundred and ten SNPs, each unique to one of the six strains, were used to genotype 150 additional isolates by applying DNA mass spectrometry. Lineage-specific SNPs were identified that could distinguish the major lineages of the clinical isolates. A subset including 32 SNPs was found to be sufficient to type four major groups of MTB isolates in Taiwan (ancient Beijing, modern Beijing, East African–Indian, and Latin-American Mediterranean). However, there was high genetic homozygosity within the Euro-American lineage, which included spoligotype-classified Haarlem and T strains. By whole-genome sequencing of 12 representative Euro-American isolates, we identified multiple subtype-specific SNPs which allowed us to distinguish two major branches within the Euro-American lineage.

show abstract

Draft Genome Sequences of the Mycobacterium tuberculosis Clinical Strains A2 and A4, Isolated from a Relapse Patient in Taiwan

Cited by 3 publications

References 9 publications

MIRU-profiler: a rapid tool for determination of 24-loci MIRU-VNTR profiles from assembled genomes ofMycobacterium tuberculosis

MIRU-profiler: a rapid tool for determination of 24-loci MIRU-VNTR profiles from assembled genomes ofMycobacterium tuberculosis

Genomics Study of Mycobacterium tuberculosis Strains from Different Ethnic Populations in Taiwan

Lineage-specific SNPs for genotyping of Mycobacterium tuberculosis clinical isolates

Contact Info

Product

Resources

About