Functional Analysis Using Whole-Genome Sequencing of a Drug-Sensitive Mycobacterium tuberculosis Strain from Peru

Tarazona, David; Borda, Víctor; Galarza, Marco; Agapito, Juan; Guio, Heinner

doi:10.1128/genomea.00087-14

Cited by 2 publications

(2 citation statements)

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“…Se construyeron librerías genómicas de extremos pareados, las cuales fueron secuenciadas en el equipo HiSeq 2000, Illumina (Macrogen, Korea) (15)(16)(17) , siguiendo los protocolos del fabricante. El ensamblaje de la secuenciación de lecturas se llevó a cabo por el software BWA versión v 0.5.9-r16, usando el genoma referencial H37Rv.…”

Section: Datos Genómicos De Cepas De Mycobacterium Tuberculosisunclassified

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Análisis genómico comparativo de cepas peruanas de Mycobacterium tuberculosis

Tarazona

Galarza

Levano

et al. 2016

Rev Peru Med Exp Salud Publica

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Objetivos. Analizar comparativamente tres secuencias genómicas de Mycobacterium tuberculosis (MTB): INS-SEN, cepa sensible; INS-MDR, cepa multidrogorresistente e INS-XDR, cepa extensamente resistente, procedentes de la Ciudad de Lima, Perú. Materiales y métodos. Se identificaron los polimorfismos de un solo nucleótido (SNPs) específicos en las cepas INS-SEN, INS-MDR y INS-XDR mediante el criterio de inclusión/exclusión. Se compararon los tres genomas de MTB y se construyó una filogenia molecular con 27 cepas de MTB de otros estudios, disponibles de la base de datos Genbank. Los SNPs específicos en cada genoma fueron organizados en clústers de grupos ortólogos (COGs). Resultados. El análisis de genomas permitió identificar un conjunto de SNPs asociados a determinantes de virulencia (familia de proteínas mce, policetidos, phiRv1, transposasas, metiltransferasas y relacionados a síntesis de vitaminas) principalmente. Se observa una estrecha relación entre la cepa INS-MDR y INS-XDR, con solo un 6,1% de SNPs diferentes, sin embargo, la cepa INS-SEN presenta un 50,2 y 50,3% de SNPs diferentes a las cepas MDR y XDR, respectivamente. La filogenia molecular agrupó a las cepas peruanas dentro del linaje LAM y cercanamente a las cepas F11 y KZN de Sudáfrica. Conclusiones. Se evidenció una alta similitud (99,9%) de la cepa INS-SEN con la cepa sudafricana F11, de gran alcance mundial, mientras los análisis de las cepas INS-MDR e INS-XDR demuestran una probable expansión de la familia KZN, cepa de Sudáfrica con alta virulencia y patogenicidad.Palabras clave: Tuberculosis; Genómica; Farmacorresistencia bacteriana (fuente: DeCS BIREME). COMPARATIVE GENOMIC ANALYSIS OF PERUVIAN STRAINS OF Mycobacterium tuberculosis ABSTRACT Objectives. To comparatively analyze three genomic sequences of Mycobacterium tuberculosis (MTB), including sensitive (INS-SEN), multi-drug-resistant (INS-MDR), and extremely drug-resistant (INS-XDR) strains, collected in Lima,Peru. Materials and Methods. Specific single nucleotide polymorphisms (SNPs) were identified in the INS SEN, INS-MDR, and INS-XDR strains according to the inclusion/exclusion criteria. The three MTB genomes were compared and a molecular phylogeny was constructed with 27 MTB strains from other studies available from the Genbank database. Results. The specific SNPs in each genome were organized in clusters of orthologous groups (COGs). The genomic analysis allowed for the identification of a set of SNPs associated mainly with virulence determinants (family of mce proteins, polyketides, phiRv1, transposase, and methyltransferases, and other related to vitamin synthesis). A close correlation between the INS-MDR and INS-XDR strains was observed, with only a 6.1% difference in SNPs; however, the INS-SEN strain had 50.2% and 50.3% different SNPs from the MDR and XDR strains, respectively. The molecular phylogeny grouped the Peruvian strains within the LAM lineage and closely to the F11 and KZN strains from South Africa. Conclusions. High similarity (99.9%) was noted between the INS-SEN strain ...

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Section: Datos Genómicos De Cepas De Mycobacterium Tuberculosisunclassified

“…Determinamos los SNPs estrechamente relacionados a MTB H37Rv (AL123456.2) mediante los programas SamTools, SNPtree y scripts en Perl para INS-SEN (15) , INS-MDR (16) e INS-XDR (17) . …”

Section: Análisis De Secuencias Y Filogenia Molecularunclassified

Análisis genómico comparativo de cepas peruanas de Mycobacterium tuberculosis

Tarazona

Galarza

Levano

et al. 2016

Rev Peru Med Exp Salud Publica

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The Peruvian Genome Project: expanding the global pool of genome diversity from South America

Guio,

Caceres,

Sanchez

et al. 2024

Preprint

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The process of inhabiting the Americas by ancestral native American populations involved many individuals settling in the Peruvian Andes and Amazonian regions. Due to Latin American countries representing less than 1% of the human genome data available in public reference databases, the evolution and migration processes involved in adapting to this unique geography have not yet been fully explained. The Peruvian Genome Project is an initiative first of its kind, started in 2011, to address the underrepresentation of genomic data from native South American populations. This project has collected to date 1,149 samples from 17 traditional native and 13 mestizo (mixed of native, African, and European ancestry) communities. Currently, 150 whole genomes and 873 array-genotyped individuals have been sequenced from across the geography of Western South America, including coastal, Andes, and Amazonian regions. We discovered 1.6 million novel genetic variants with varying frequencies, indicative of local environmental adaptations and population drift. These novel variants allow us to infer local evolutionary traits and population-specific allele frequencies for people living at different altitudes, as well as varying adaptations to pathogens and living conditions. The Peruvian Genome Project is the result of more than a decade of work in sample selection, logistics, and approved regulatory community engagement, designed to enhance the human genome pool of diversity of native Americans. The data collected here enable the targeted characterization of endemic diseases, trait adaptations, and new variants of clinical significance in South America. The Peruvian Genome Project represents a step forward in international and multidisciplinary efforts to make precision medicine more inclusive and accessible for underrepresented communities in Latin America, offering significant potential for drug development and diagnostics in a neglected continent.

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Functional Analysis Using Whole-Genome Sequencing of a Drug-Sensitive Mycobacterium tuberculosis Strain from Peru

Cited by 2 publications

References 10 publications

Análisis genómico comparativo de cepas peruanas de Mycobacterium tuberculosis

Análisis genómico comparativo de cepas peruanas de Mycobacterium tuberculosis

The Peruvian Genome Project: expanding the global pool of genome diversity from South America

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