Genetic diversity of Mycobacterium tuberculosis from Pará, Brazil, reveals a higher frequency of ancestral strains than previously reported in South America

Conceição, Emilyn Costa; Rastogi, Nalin; Couvin, David; Lopes, Maria Luíza; Furlaneto, Ismari Perini; Gomes, Harrison Magdinier; Vasconcellos, Sidra Ezídio Gonçalves; Suffys, Philip Noël; Schneider, Maria Paula Cruz; Sousa, Maísa Silva de; Sola, Christophe; Guimarães, Ricardo José de Paula Souza e; Duarte, Rafael Silva; Lima, Karla Valéria Batista

doi:10.1016/j.meegid.2017.10.021

Cited by 13 publications

(18 citation statements)

References 38 publications

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“…The SIT292 (which is predominantly found in Myanmar and Bangladesh, representing respectively 9.03% and 7.52% of isolates in these countries), could be potentially relabeled as EAI6-MMR. Another pattern, SIT129/EAI6-BGD1, described in a recent paper by Conceição et al (2017) [38], seemed to be specific to Mozambique. SIT2934/EAI2-Manila was predominantly linked to 12-MIT1154 ( S4 Fig ), and this spoligotyping pattern was found exclusively in Trinidad and Tobago.…”

Section: Resultsmentioning

confidence: 96%

Two tales: Worldwide distribution of Central Asian (CAS) versus ancestral East-African Indian (EAI) lineages of Mycobacterium tuberculosis underlines a remarkable cleavage for phylogeographical, epidemiological and demographical characteristics

2019

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The East African Indian (EAI) and Central Asian (CAS) lineages of Mycobacterium tuberculosis complex (MTBC) mainly infect tuberculosis (TB) patients in the eastern hemisphere which contains many of the 22 high TB burden countries including China and India. We investigated if phylogeographical, epidemiological and demographical characteristics for these 2 lineages differed in SITVIT2 database. Genotyping results and associated data (age, sex, HIV serology, drug resistance) on EAI and CAS lineages (n = 10,974 strains) were extracted. Phylogenetic and Bayesian, and other statistical analyses were used to compare isolates. The male/female sex ratio was 907/433 (2.09) for the EAI group vs. 881/544 (1.62) for CAS (p-value<0.002). The proportion of younger patients aged 0–20 yrs. with CAS lineage was significantly higher than for EAI lineage (18.07% vs. 10.85%, p-value<0.0001). The proportion of multidrug resistant and extensively drug resistant TB among CAS group (30.63% and 1.03%, respectively) was significantly higher than in the EAI group (12.14% and 0.29%, respectively; p-value<0.0001). Lastly, the proportion of HIV+ patients was 20.34% among the EAI group vs. 3.46% in the CAS group (p-value<0.0001). This remarkable split observed between various parameters for these 2 lineages was further corroborated by their geographic distribution profile (EAI being predominantly found in Eastern-Coast of Africa, South-India and Southeast Asia, while CAS was predominantly found in Afghanistan, Pakistan, North India, Nepal, Middle-east, Libya, Sudan, Ethiopia, Kenya and Tanzania). Some geo-specificities were highlighted. This study demonstrated a remarkable cleavage for aforementioned characteristics of EAI and CAS lineages, showing a North-South divide along the tropic of cancer in Eastern hemisphere–mainly in Asia, and partly prolonged along the horn of Africa. Such studies would be helpful to better comprehend prevailing TB epidemic in context of its historical spread and evolutionary features, and provide clues to better treatment and patient-care in countries and regions concerned by these lineages.

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Section: Resultsmentioning

confidence: 96%

Two tales: Worldwide distribution of Central Asian (CAS) versus ancestral East-African Indian (EAI) lineages of Mycobacterium tuberculosis underlines a remarkable cleavage for phylogeographical, epidemiological and demographical characteristics

2019

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“…Numerical closeness of RSCU values between coding sequences shows the closeness of relationship [ 28 ]. Genetic diversity of Mycobacterium tuberculosis from different area may have different frequency of ancestral strains [ 29 ]. Diversity and disease pathogenesis for Mycobacterium tuberculosis from different area may show difference too [ 30 , 31 ].…”

Section: Resultsmentioning

confidence: 99%

Comprehensive Analysis and Comparison on the Codon Usage Pattern of Whole Mycobacterium tuberculosis Coding Genome from Different Area

Ren

Haixian

et al. 2018

BioMed Research International

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Phenomenon of unequal use of synonymous codons in Mycobacterium tuberculosis is common. Codon usage bias not only plays an important regulatory role at the level of gene expression, but also helps in improving the accuracy and efficiency of translation. Meanwhile, codon usage pattern of Mycobacterium tuberculosis genome is important for interpreting evolutionary characteristics in species. In order to investigate the codon usage pattern of the Mycobacterium tuberculosis genome, 12 Mycobacterium tuberculosis genomes from different area are downloaded from the GeneBank. The correlations between G3, GC12, whole GC content, codon adaptation index, codon bias index, and so on of Mycobacterium tuberculosis genomes are calculated. The ENC-plot, relationship between A3/(A3 + T3) and G3/(G3 + C3), GC12 versus GC3 plot, and the RSCU of overall/separated genomes all show that the codon usage bias exists in all 12 Mycobacterium tuberculosis genomes. Lastly, relationship between CBI and the equalization of ENC shows a strong negative correlation between them. The relationship between protein length and GC content (GC3 and GC12) shows that more obvious differences in the GC content may be in shorter protein. These results show that codon usage bias existing in the Mycobacterium tuberculosis genomes could be used for further study on their evolutionary phenomenon.

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“…Compared the DR of Lineage 1 in the context of other lineages from the same region, the most predominant was Lineage 4, among of which T and X lineages, were associated to MDR-TB, while Lineage 1 the highest among 'any resistance' group. (2) Among all in silico based tools tested presently, we encountered difficulties to predict resistance to PZA, which can be partly due to alternative mechanisms of resistance to this drug (non pncA related) (21) and reports of low-frequency SNPs that may be associated with PZA resistance. (22) In the present study however, we did not include PZA in the conventional DST, a major limitation of the study.…”

Section: Discussionmentioning

confidence: 99%

“…Sampling -Out of 980 M. tuberculosis isolates from the state of Pará, Brazil, 97 were classified as East-African-Indian (EAI) by Spoligotyping, (2) among which 71 were recovered and classified as Lineage 1 (3) were used in this present study for DR evaluation.…”

Section: Methodsmentioning

confidence: 99%

“…(1) Lineage 1 is infrequently reported in South America except for one study that described 98 such strains in Northern Brazil, representing 10% of the study population. (2) Through single nucleotide polymorphism (SNP) typing, we hypothesised to have been introduced during the trans-Atlantic slave trade. (3) The L1 has not been associated to the drug resistance (DR), (4) different to L2 and L4 that are strongly associated with DR. (4) We therefore determined the DR profile using the conventional phenotypical antimicrobial drug susceptibility tests (DST) and compared that with in silico DR prediction on whole-genome sequencing (WGS) of 71 isolates of M. tuberculosis L1 from Pará generated presently, together with three isolates with recently published genomes.…”

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confidence: 99%

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Evaluation of drug susceptibility profile of Mycobacterium tuberculosis Lineage 1 from Brazil based on whole genome sequencing and phenotypic methods

Guimarães

Sharma

Furlaneto

et al. 2020

Mem. Inst. Oswaldo Cruz

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Genetic diversity of Mycobacterium tuberculosis from Pará, Brazil, reveals a higher frequency of ancestral strains than previously reported in South America

Cited by 13 publications

References 38 publications

Two tales: Worldwide distribution of Central Asian (CAS) versus ancestral East-African Indian (EAI) lineages of Mycobacterium tuberculosis underlines a remarkable cleavage for phylogeographical, epidemiological and demographical characteristics

Two tales: Worldwide distribution of Central Asian (CAS) versus ancestral East-African Indian (EAI) lineages of Mycobacterium tuberculosis underlines a remarkable cleavage for phylogeographical, epidemiological and demographical characteristics

Comprehensive Analysis and Comparison on the Codon Usage Pattern of Whole Mycobacterium tuberculosis Coding Genome from Different Area

Evaluation of drug susceptibility profile of Mycobacterium tuberculosis Lineage 1 from Brazil based on whole genome sequencing and phenotypic methods

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