Annotated Genome Sequences of 16 Lineage 4 Mycobacterium tuberculosis Strains from Guatemala.

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