ABSTRACT
Whole-genome sequencing has resulted in new insights into the phylogeography of Mycobacterium tuberculosis. However, only limited genomic data are available from M. tuberculosis strains in Guatemala. Here we report 16 complete genomes of clinical strains belonging to the Euro-American lineage 4, the most common lineage found in Guatemala and Central America.
GENOME ANNOUNCEMENT
Genome sequencing has revealed much about the phylogeography of Mycobacterium tuberculosis, wherein discrete genetic lineages of this human pathogen associate with specific regions of the world. While many isolates have been sequenced from a variety of locales, limited genomic sequence data are available regarding M. tuberculosis strains in Guatemala. Previously, we reported on the presence of East Asian lineage 2 strains in Guatemala in an urban setting (1). However, throughout Central and South America, Euro-American lineage 4 strains are most common (2). Here we report 16 complete genomes of Euro-American lineage 4 strains. Isolates were collected at the Clínica Familiar Luis Angel García (CFLAG), an HIV-specialized clinic associated with the Hospital General San Juan de Dios in Guatemala City.
Cultures were grown on Lowenstein-Jensen medium. Genomic DNA was extracted using a modified protocol of the ArchivePure DNA cell/tissue purification kit (5 Prime GmbH, Germany). Spoligotyping was carried out using the spoligotyping kit and protocol from Isogen Biosolutions (Ocimum Biosolutions Ltd., India), identifying the isolates as lineage 4 strains. Paired-end 50-bp reads were sequenced on the Illumina HiSeq 2500 platform to depths ranging from 327- to 627-fold coverage. Reads were aligned against the H37Rv reference genome (GenBank accession number NC_000962) using Burrows-Wheeler alignment (3). Variants were called with SAMtools (4) and filtered with VarScan (5) for a minimum read depth of 10, a consensus quality score of 20, and a minimum variant frequency of 0.75. Single nucleotide polymorphisms (SNPs) adjacent to indels and within repetitive regions of the genome were discarded. Neighbor-joining and maximum-likelihood methods of phylogeny construction based on genome-wide SNPs placed the Guatemalan isolates among known lineage 4 strains, confirming the spoligotyping results. Consensus sequences for each isolate were generated using BCFtools (6), and gene annotations were added by the NCBI Prokaryotic Genome Annotation Pipeline.
Accession number(s).
The genome sequences of the M. tuberculosis isolates reported here have been deposited in GenBank under the accession numbers listed in Table 1.
TABLE 1.
Genome sequence data for 16 lineage 4 M. tuberculosis strains from Guatemala
| Strain | GenBank accession no. | Sequencing depth (×) | Genome size (bp) |
|---|---|---|---|
| GG-111-10 | CP025593 | 539.6 | 4,411,563 |
| GG-5-10 | CP025594 | 496.0 | 4,411,442 |
| GG-20-11 | CP025595 | 403.2 | 4,411,504 |
| GG-27-11 | CP025596 | 565.5 | 4,411,443 |
| GG-36-11 | CP025597 | 557.2 | 4,411,469 |
| GG-37-11 | CP025598 | 530.7 | 4,411,526 |
| GG-45-11 | CP025599 | 464.7 | 4,411,469 |
| GG-77-11 | CP025600 | 627.0 | 4,411,508 |
| GG-90-10 | CP025601 | 522.9 | 4,411,602 |
| GG-109-10 | CP025602 | 550.3 | 4,411,463 |
| GG-121-10 | CP025603 | 526.2 | 4,411,510 |
| GG-129-11 | CP025604 | 525.2 | 4,411,413 |
| GG-134-11 | CP025605 | 551.0 | 4,411,399 |
| GG-137-10 | CP025606 | 475.6 | 4,411,446 |
| GG-186-10 | CP025607 | 327.6 | 4,411,478 |
| GG-229-10 | CP025608 | 557.2 | 4,411,519 |
ACKNOWLEDGMENTS
This work was supported by the Asociación de Salud Integral (Guatemala), a National Science Foundation Graduate Research Fellowship (J.W.S.), and a Whitehead Scholar Award (D.M.T.) and approved by the Institutional Ethics Committee of the Hospital San Juan de Dios (Guatemala).
Patient information was collected and maintained exclusively in Guatemala; genome sequencing and analysis of deidentified samples were performed at Duke.
Footnotes
Citation Saelens JW, Lau-Bonilla D, Moller A, Xet-Mull AM, Medina N, Guzmán B, Calderón M, Herrera R, Stout JE, Arathoon E, Samayoa B, Tobin DM. 2018. Annotated genome sequences of 16 lineage 4 Mycobacterium tuberculosis strains from Guatemala. Genome Announc 6:e00024-18. https://doi.org/10.1128/genomeA.00024-18.
REFERENCES
- 1.Saelens JW, Lau-Bonilla D, Moller A, Medina N, Guzmán B, Calderón M, Herrera R, Sisk DM, Xet-Mull AM, Stout JE, Arathoon E, Samayoa B, Tobin DM. 2015. Whole genome sequencing identifies circulating Beijing-lineage Mycobacterium tuberculosis strains in Guatemala and an associated urban outbreak. Tuberculosis (Edinb) 95:810–816. doi: 10.1016/j.tube.2015.09.001. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2.Stucki D, Brites D, Jeljeli L, Coscolla M, Liu Q, Trauner A, Fenner L, Rutaihwa L, Borrell S, Luo T, Gao Q, Kato-Maeda M, Ballif M, Egger M, Macedo R, Mardassi H, Moreno M, Tudo Vilanova G, Fyfe J, Globan M, Thomas J, Jamieson F, Guthrie JL, Asante-Poku A, Yeboah-Manu D, Wampande E, Ssengooba W, Joloba M, Henry Boom W, Basu I, Bower J, Saraiva M, Vaconcellos SEG, Suffys P, Koch A, Wilkinson R, Gail-Bekker L, Malla B, Ley SD, Beck HP, de Jong BC, Toit K, Sanchez-Padilla E, Bonnet M, Gil-Brusola A, Frank M, Penlap Beng VN, Eisenach K, Alani I, Wangui Ndung'u P, Revathi G, Gehre F, Akter S, Ntoumi F, Stewart-Isherwood L, Ntinginya NE, Rachow A, Hoelscher M, Cirillo DM, Skenders G, Hoffner S, Bakonyte D, Stakenas P, Diel R, Crudu V, Moldovan O, Al-Hajoj S, Otero L, Barletta F, Jane Carter E, Diero L, Supply P, Comas I, Niemann S, Gagneux S. 2016. Mycobacterium tuberculosis lineage 4 comprises globally distributed and geographically restricted sublineages. Nat Genet 48:1535–1543. doi: 10.1038/ng.3704. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3.Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754–1760. doi: 10.1093/bioinformatics/btp324. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4.Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25:2078–2079. doi: 10.1093/bioinformatics/btp352. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5.Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, Weinstock GM, Wilson RK, Ding L. 2009. VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics 25:2283–2285. doi: 10.1093/bioinformatics/btp373. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.Danecek P, McCarthy SA. 2017. BCFtools/csq: haplotype-aware variant consequences. Bioinformatics 33:2037–2039. doi: 10.1093/bioinformatics/btx100. [DOI] [PMC free article] [PubMed] [Google Scholar]