Strain-specific estimation of epidemic success provides insights into the transmission dynamics of tuberculosis

Rasigade, Jean‐Philippe; Barbier, Maxime; Dumitrescu, Oana; Pichat, Catherine; Carret, G.; Ronnaux-Baron, Anne-Sophie; Blasquez, Ghislaine; Godin-Benhaïm, Christine; Boisset, Sandrine; Carricajo, Anne; Jacomo, Véronique; Frédénucci, Isabelle; Montclos, Michèle Pérouse de; Ader, Florence; Supply, Philip; Lina, Gérard; Wirth, Thierry

doi:10.1038/srep45326

Cited by 20 publications

(50 citation statements)

References 51 publications

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“…The aim of this paper was to investigate whether mercury pollution may explain the success of USA 300-LV in South America, notably in the Andean countries where the high prevalence of USA300-LV (9)(10)(11)(12) coincides with high environmental mercury pollution (15). Using the Timescaled Haplotypic Density (THD) method to examine patterns of epidemic success (17) in 250 genomes of the ST8 lineage, we confirmed that the acquisition of mecA, followed by COMER or ACME contributed to epidemic success of the two sub-lineages, and that COMER only increased success in South American countries. In vitro experiments in the presence of subinhibitory concentration of mercury revealed an overexpression of major virulence factors by USA300-LV and a fitness advantage of USA-LV over USA300-NA, thus providing a plausible model and selection drive explaining the success of USA300-LV in South America.…”

Section: Introductionmentioning

confidence: 67%

“…We compared the evolution of epidemic success in the two USA300 sublineages using timescaled haplotypic density (THD) (17). The THD method uses pairwise genetic distances to estimate the epidemic success of each isolate in a collection, allowing comparisons of success based on various isolate characteristics.…”

Section: The Epidemic Success Of the St8 Lineage Increases Sequentialmentioning

confidence: 99%

“…The THD method uses pairwise genetic distances to estimate the epidemic success of each isolate in a collection, allowing comparisons of success based on various isolate characteristics. THD approaches have been successfully applied to investigate drivers of epidemic success in bacterial pathogens including Staphylococci (17,(21)(22)(23). Applied to 250 genomes of ST8 (combining those previously analyzed by (20) completed by 21 USA300-LV from our collection), the method revealed several important features: (i) the acquisition of the Panton-Valentine leucocidin gene by the ancestral ST8 clearly boosted the epidemic success of the lineage (Fig.…”

Section: The Epidemic Success Of the St8 Lineage Increases Sequentialmentioning

confidence: 99%

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Potential role of Mercury pollutants in the success of Methicillin-ResistantStaphylococcus aureusUSA300 in Latin America

Gustave

Rasigade

Martins-Simões

et al. 2020

Preprint

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AbstractCommunity-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) lineage known as USA300-North American (NA) has become highly prevalent in North America whilst a USA300 variant known as USA300-LV, harboring a mercury resistance element (COMER), has become dominant in South America. We investigated whether mercury pollution, which is common in South America notably because of artisanal gold mining, may explain the local dominance pattern of USA300-LV. Density-based estimation of epidemic success in 250 genomes of the ST8 lineage revealed that the acquisition of COMER in USA300 progenitors increased success in South American countries but decreased success elsewhere. The fitness of USA300-LV was impaired in vitro compared with USA300-NA, but the addition of sub-inhibitory concentration of mercury provided a strong fitness advantage to USA300-LV and triggered an overexpression of major virulence factors. The success of USA300-LV in South America may result from low-level mercury exposure selecting resistant and virulent strains.

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Section: Introductionmentioning

confidence: 67%

Section: The Epidemic Success Of the St8 Lineage Increases Sequentialmentioning

confidence: 99%

Section: The Epidemic Success Of the St8 Lineage Increases Sequentialmentioning

confidence: 99%

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Potential role of Mercury pollutants in the success of Methicillin-ResistantStaphylococcus aureusUSA300 in Latin America

Gustave

Rasigade

Martins-Simões

et al. 2020

Preprint

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“…It is widely recognized that Mycobacterium tuberculosis (Mtb) of different molecular types have different transmission capacities, pathogenicity and drug resistance rates [1,2]. Therefore, Mtb genotypes may be associated with the tuberculosis (TB) endemicity [3,4]. Guangxi Zhuang Autonomous…”

Section: Introductionmentioning

confidence: 99%

The geno-spatio analysis of Mycobacterium tuberculosis complex in hot and cold spots of Guangxi, China

Lin

Cui

Virasakdi

et al. 2020

Preprint

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Abstract Background At present, there are few studies on polymorphism of Mycobacterium tuberculosis (Mtb) gene and how it affects the TB epidemic. This study aimed to document the differences of polymorphisms between tuberculosis hot and cold spot areas of Guangxi Zhuang Autonomous Region, China. Methods The cold and hot spot areas, each with 3 counties, had been pre-identified by TB incidence for 5 years from the surveillance database. Whole genome sequencing analysis was performed on all sputum Mtb isolates from the detected cases during January and June 2018. Single nucleotide polymorphism (SNP) of each isolate compared to the H37Rv strain were called and used for lineage and sub-lineage identification. Pairwise SNP differences between every pair of isolates were computed. Analyses of Molecular Variance (AMOVA) across counties of the same hot or cold spot area and between the two areas were performed. Results As a whole, 59.8% (57.7% sub-lineage 2.2 and 2.1% sub-lineage 2.1) and 39.8% (17.8% sub-lineage 4.4, 6.5% sub-lineage 4.2 and 15.5% sub-lineage 4.5) of the Mtb strains were Lineage 2 and Lineage 4 respectively. The percentages of sub-lineage 2.2 (Beijing family strains) are significantly higher in hot spots. Through the MDS dimension reduction, the genomic population structure in the three hot spot counties is significantly different from those three cold spot counties (T-test p = 0.05). The median of SNPs distances among Mtb isolates in cold spots was greater than that in hot spots (897 vs 746, Rank-sum test p < 0.001). Three genomic clusters, each with genomic distance ≤ 12 SNPs, were identified with 2, 3 and 4 consanguineous strains. Two clusters were from hot spots and one was from cold spots. Conclusion Narrower genotype diversity in the hot area may indicate higher transmissibility of the Mtb strains in the area compared to those in the cold spot area.

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“…Lineage 4 represents the most diverse and geographically widespread lineage of M. tuberculosis, with each sub-lineage having different phenotypic characteristics (Rasigade et al, 2017, Comas et al, 2014, Stucki et al, 2016. Major sub-lineages within lineage 4 include X, T, Latin American Mediterranean (LAM) and Haarlem (Fitzgibbon et al, 2013).…”

Section: 13: M Tuberculosis Sub-lineagesmentioning

confidence: 99%

Use of Whole Genome Sequencing in Understanding Transmission Dynamics of Tuberculosis

Jones¹

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Mycobacterium tuberculosis is the leading cause of death from an infectious disease worldwide. An understanding of tuberculosis transmission dynamics in outbreak settings is vital for its control. The advent of affordable whole genome sequencing (WGS) has provided scope for superior resolution of tuberculosis outbreaks, compared to previous methods. However, the challenge lies in standardising the vast quantities of resulting data in a structured manner which lends itself to easy comparison of isolates. Gene-by-gene Multi-Locus Sequence Typing (MLST) methods of analysing WGS data, as opposed to Single Nucleotide Polymorphism (SNP) mapping, have shown promise in providing a uniform platform for outbreak resolution. WGS was performed on clinical isolates from three M. tuberculosis outbreaks in South West Wales. Molecular typing by MIRU-VNTR and epidemiological investigation had resulted in conflicting conclusions. Outbreak analysis and phylogenetic typing of all isolates was carried out using the WGS gene-by-gene MLST analysis method of core genome MLST (cgMLST) and traditional WGS SNP mapping. Where DNA quality was unsatisfactory, an ancient DNA library preparation was used successfully. Provean and BEAST software analysis provided physiological

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Strain-specific estimation of epidemic success provides insights into the transmission dynamics of tuberculosis

Cited by 20 publications

References 51 publications

Potential role of Mercury pollutants in the success of Methicillin-ResistantStaphylococcus aureusUSA300 in Latin America

Potential role of Mercury pollutants in the success of Methicillin-ResistantStaphylococcus aureusUSA300 in Latin America

The geno-spatio analysis of Mycobacterium tuberculosis complex in hot and cold spots of Guangxi, China

Use of Whole Genome Sequencing in Understanding Transmission Dynamics of Tuberculosis

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