Genetic diversity of Mycobacterium tuberculosis and transmission associated with first-line drug resistance: a first analysis in Jalisco, Mexico

Lopez-Avalos, Gladys; Gonzalez-Palomar, Guadalupe; Lopez-Rodriguez, Martín; Vazquez-Chacon, Carlos A.; Mora-Aguilera, Gustavo; González-Barrios, Juan Antonio; Villanueva-Arias, Juan Carlos; Sandoval-Díaz, Manuel; Miranda-Hernández, Ulises; Álvarez-Maya, Ikuri

doi:10.1016/j.jgar.2017.07.004

Cited by 14 publications

(12 citation statements)

References 36 publications

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“…However, the most used genes as markers, according to studies, such as a recent systematic review (Seifert et al), (18) which evaluated 11.411 M. tuberculosis isolates in 49 countries (January 2000 to August 2013), are the katG (315 G/C) and the inhA (-15 C/T) promoter region. Confirming these findings, we also have the study of Monteserin et al, (19) who evaluated the same markers to analyse the drug resistance profile of INH and the distribution of clusters in Argentina, as well as the study of Lopez-Avalos et al, (20) which used the same markers to identify the resistance already described.…”

Section: Discussionsupporting

confidence: 74%

Rapid detection of Mycobacterium tuberculosis DNA and genetic markers for Isoniazid resistance in Ziehl-Neelsen stained slides

Bello

Morais

Jesus

et al. 2020

Mem. Inst. Oswaldo Cruz

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BACKGROUND Early diagnosis of tuberculosis (TB) and identification of strains of Mycobacterium tuberculosis resistant to anti-TB drugs are considered the main factors for disease control. OBJECTIVES To standardise a real-time polymerase chain reaction (qPCR) assay technique and apply it to identify mutations involved in M. tuberculosis resistance to Isoniazid (INH) directly in Ziehl-Neelsen (ZN) stained slides. METHODS Were analysed 55 independent DNA samples extracted from clinical isolates of M. tuberculosis by sequencing. For application in TB diagnosis resistance, 59 ZN-stained slides were used. The sensitivity, specificity and Kappa index, with a 95% confidence interval (CI95%), were determined. FINDINGS The agreement between the tests was, for the katG target, the Kappa index of 0.89 (CI95%: 0.7-1.0). The sensitivity and specificity were 97.6% (CI95%: 87.7-99.9) and 91.7% (CI95%: 61.5-99.5), respectively. For inhA, the Kappa index was 0.92 (CI95%: 0.8-1.0), the sensitivity and specificity were 94.4% (CI95%: 72.7-99.8) and 97.3% (CI95%: 85.8-99.9), respectively. The use of ZNstained slides for drug-resistant TB detection showed significant results when compared to other standard tests for drug resistance. MAIN CONCLUSIONS qPCR genotyping proved to be an efficient method to detect genes that confer M. tuberculosis resistance to INH. Thus, qPCR genotyping may be an alternative instead of sequencing.

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Section: Discussionsupporting

confidence: 74%

Rapid detection of Mycobacterium tuberculosis DNA and genetic markers for Isoniazid resistance in Ziehl-Neelsen stained slides

Bello

Morais

Jesus

et al. 2020

Mem. Inst. Oswaldo Cruz

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“…Many factors may affect the codon usage in Mycobacterium tuberculosis , such as mutation pressure [ 12 ], gene length [ 13 ], and natural selection [ 14 ]. Most previous studies deal with the relatively smaller set of Mycobacterium tuberculosis isolates [ 15 , 16 ] or the isolates from one area [ 17 , 18 ]. In this paper, genetic diversity of Mycobacterium tuberculosis from 12 areas is compared and analyzed.…”

Section: Introductionmentioning

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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“…Previous reports have also indicated that in areas with low prevalence of TB high genetic diversity is expected (Lopez-Avalos et al, 2017;Michel et al, 2008) since the dominance and transmission of a single strain is less likely, rather TB in such settings is the result of reactivation from previous infections. This is substantiated in the current study by the fact that there were 69 spoligotype patterns from the 177 M. tuberculosis isolates typed.…”

Section: Discussionmentioning

confidence: 99%

Spoligotype‐based population structure of Mycobacterium tuberculosis in the Jimma Zone, southwest Ethiopia

et al. 2018

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Background To understand the population dynamics and propose more effective preventive strategies, defining the population structure of the circulating Mycobacterium tuberculosis strains is important. Methods A total of 177 M. tuberculosis complex isolates from pulmonary tuberculosis (TB) cases in southwest Ethiopia were genotyped by spoligotyping. Of the strains included in this study, 126 were pan‐susceptible strains while the remaining 51 isolates were resistant to one or more first‐line anti‐TB drugs. The genotyping results were compared to the international spoligotyping (SITVIT) database of the Pasteur Institute of Guadeloupe and the newly revised publicly available international multi‐marker database (SITVITWEB/SPOLDB4). An online tool Run TB‐Lineage was also used to predict the major lineages using a conformal Bayesian network analysis. Results The spoligotyping of the 177 isolates resulted in 69 different spoligotype patterns of which 127 (71.8%) were clustered into 19 spoligoclusters (with clustering rate of 61.02%). Each cluster contains 2–29 isolates. Of the isolates with corresponding SIT in SITVIT/SDB4, the predominant strains identified were SIT 37 of the T3 subfamily with 29 isolates followed by SIT 53 of the T1 subfamily with 20 isolates. SIT 777 of the H4 subfamily and SIT 25 of the CAS1_DELHI subfamily each consisting of six isolates were identified. Eighty spoligotype patterns were orphan as they were not recorded in the SITVIT2/SPDB4 database. Further classification of the isolates on the basis of major lineages showed that 82.5% and 14.1% of the isolates belonged to Euro‐American and East African Indian lineages, respectively, while 2.8% of the isolates belonged to Mycobacterium africanum and 0.6% to Indo‐Oceanic. Conclusion The ill‐defined T and H clades were predominant around Jimma. The substantial number of orphans recorded in the study area warrants for additional studies with genotyping methods with better resolution and covering whole areas of southwest Ethiopia.

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Genetic diversity of Mycobacterium tuberculosis and transmission associated with first-line drug resistance: a first analysis in Jalisco, Mexico

Abstract: This study using spoligotyping and MIRU-VNTR showed that the analysed strains were not related to each other since no two identical strains were found. Families with the highest prevalence in the study were orphans followed by T family.

Cited by 14 publications

References 36 publications

Rapid detection of Mycobacterium tuberculosis DNA and genetic markers for Isoniazid resistance in Ziehl-Neelsen stained slides

Rapid detection of Mycobacterium tuberculosis DNA and genetic markers for Isoniazid resistance in Ziehl-Neelsen stained slides

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

Spoligotype‐based population structure of Mycobacterium tuberculosis in the Jimma Zone, southwest Ethiopia

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