Comparative genomics of Mycobacterium africanum Lineage 5 and Lineage 6 from Ghana suggests distinct ecological niches

Isaac Darko Otchere; Mireia Coscollá; Leonor Sánchez-Busó; Adwoa Asante-Poku; Daniela Brites; Chloe Loiseau; Conor Meehan; Stephen Osei-Wusu; Audrey Forson; Clement Laryea; Abdallah Iddrisu Yahayah; Akosua Baddoo; Gloria Akosua Ansa; Samuel Yaw Aboagye; Prince Asare; Sonia Borrell; Florian Gehre; Patrick Beckert; Thomas A. Kohl; Sanoussi N’dira; Christian Beisel; Martin Antonio; Stefan Niemann; Bouke C. de Jong; Julian Parkhill; Simon R. Harris; Sebastien Gagneux; Dorothy Yeboah-Manu

doi:10.1038/s41598-018-29620-2

Comparative genomics of Mycobacterium africanum Lineage 5 and Lineage 6 from Ghana suggests distinct ecological niches

Isaac Darko Otchere, Mireia Coscollá, Leonor Sánchez-Busó, Adwoa Asante-Poku, Daniela Brites, Chloe Loiseau, Conor Meehan, Stephen Osei-Wusu, Audrey Forson, Clement Laryea, Abdallah Iddrisu Yahayah, Akosua Baddoo, Gloria Akosua Ansa, Samuel Yaw Aboagye, Prince Asare, Sonia Borrell, Florian Gehre, Patrick Beckert, Thomas A. Kohl, Sanoussi N’diraChristian Beisel, Martin Antonio, Stefan Niemann, Bouke C. de Jong, Julian Parkhill, Simon R. Harris, Sebastien Gagneux, Dorothy Yeboah-Manu

Department of Bacteriology

Research output: Contribution to journal › Article › peer-review

32 Citations (Scopus)

Abstract

Mycobacterium africanum (Maf) causes a substantial proportion of human tuberculosis in some countries of West Africa, but little is known on this pathogen. We compared the genomes of 253 Maf clinical isolates from Ghana, including N = 175 Lineage 5 (L5) and N = 78 Lineage 6 (L6). We found that the genomic diversity of L6 was higher than in L5 despite the smaller sample size. Regulatory proteins appeared to evolve neutrally in L5 but under purifying selection in L6. Even though over 90% of the human T cell epitopes were conserved in both lineages, L6 showed a higher ratio of non-synonymous to synonymous single nucleotide variation in these epitopes overall compared to L5. Of the 10% human T cell epitopes that were variable, most carried mutations that were lineage-specific. Our findings indicate that Maf L5 and L6 differ in some of their population genomic characteristics, possibly reflecting different selection pressures linked to distinct ecological niches.

Original language	English
Article number	11269
Journal	Scientific Reports
Volume	8
Issue number	1
DOIs	https://doi.org/10.1038/s41598-018-29620-2
Publication status	Published - 1 Dec 2018

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Otchere, I. D., Coscollá, M., Sánchez-Busó, L., Asante-Poku, A., Brites, D., Loiseau, C., Meehan, C., Osei-Wusu, S., Forson, A., Laryea, C., Yahayah, A. I., Baddoo, A., Ansa, G. A., Aboagye, S. Y., Asare, P., Borrell, S., Gehre, F., Beckert, P., Kohl, T. A., ... Yeboah-Manu, D. (2018). Comparative genomics of Mycobacterium africanum Lineage 5 and Lineage 6 from Ghana suggests distinct ecological niches. Scientific Reports, 8(1), Article 11269. https://doi.org/10.1038/s41598-018-29620-2

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title = "Comparative genomics of Mycobacterium africanum Lineage 5 and Lineage 6 from Ghana suggests distinct ecological niches",

abstract = "Mycobacterium africanum (Maf) causes a substantial proportion of human tuberculosis in some countries of West Africa, but little is known on this pathogen. We compared the genomes of 253 Maf clinical isolates from Ghana, including N = 175 Lineage 5 (L5) and N = 78 Lineage 6 (L6). We found that the genomic diversity of L6 was higher than in L5 despite the smaller sample size. Regulatory proteins appeared to evolve neutrally in L5 but under purifying selection in L6. Even though over 90% of the human T cell epitopes were conserved in both lineages, L6 showed a higher ratio of non-synonymous to synonymous single nucleotide variation in these epitopes overall compared to L5. Of the 10% human T cell epitopes that were variable, most carried mutations that were lineage-specific. Our findings indicate that Maf L5 and L6 differ in some of their population genomic characteristics, possibly reflecting different selection pressures linked to distinct ecological niches.",

author = "Otchere, {Isaac Darko} and Mireia Coscoll{\'a} and Leonor S{\'a}nchez-Bus{\'o} and Adwoa Asante-Poku and Daniela Brites and Chloe Loiseau and Conor Meehan and Stephen Osei-Wusu and Audrey Forson and Clement Laryea and Yahayah, {Abdallah Iddrisu} and Akosua Baddoo and Ansa, {Gloria Akosua} and Aboagye, {Samuel Yaw} and Prince Asare and Sonia Borrell and Florian Gehre and Patrick Beckert and Kohl, {Thomas A.} and Sanoussi N{\textquoteright}dira and Christian Beisel and Martin Antonio and Stefan Niemann and {de Jong}, {Bouke C.} and Julian Parkhill and Harris, {Simon R.} and Sebastien Gagneux and Dorothy Yeboah-Manu",

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Otchere, ID, Coscollá, M, Sánchez-Busó, L, Asante-Poku, A, Brites, D, Loiseau, C, Meehan, C, Osei-Wusu, S, Forson, A, Laryea, C, Yahayah, AI, Baddoo, A, Ansa, GA, Aboagye, SY , Asare, P, Borrell, S, Gehre, F, Beckert, P, Kohl, TA, N’dira, S, Beisel, C, Antonio, M, Niemann, S, de Jong, BC, Parkhill, J, Harris, SR, Gagneux, S & Yeboah-Manu, D 2018, 'Comparative genomics of Mycobacterium africanum Lineage 5 and Lineage 6 from Ghana suggests distinct ecological niches', Scientific Reports, vol. 8, no. 1, 11269. https://doi.org/10.1038/s41598-018-29620-2

TY - JOUR

T1 - Comparative genomics of Mycobacterium africanum Lineage 5 and Lineage 6 from Ghana suggests distinct ecological niches

AU - Otchere, Isaac Darko

AU - Coscollá, Mireia

AU - Sánchez-Busó, Leonor

AU - Asante-Poku, Adwoa

AU - Brites, Daniela

AU - Loiseau, Chloe

AU - Meehan, Conor

AU - Osei-Wusu, Stephen

AU - Forson, Audrey

AU - Laryea, Clement

AU - Yahayah, Abdallah Iddrisu

AU - Baddoo, Akosua

AU - Ansa, Gloria Akosua

AU - Aboagye, Samuel Yaw

AU - Asare, Prince

AU - Borrell, Sonia

AU - Gehre, Florian

AU - Beckert, Patrick

AU - Kohl, Thomas A.

AU - N’dira, Sanoussi

AU - Beisel, Christian

AU - Antonio, Martin

AU - Niemann, Stefan

AU - de Jong, Bouke C.

AU - Parkhill, Julian

AU - Harris, Simon R.

AU - Gagneux, Sebastien

AU - Yeboah-Manu, Dorothy

PY - 2018/12/1

Y1 - 2018/12/1

N2 - Mycobacterium africanum (Maf) causes a substantial proportion of human tuberculosis in some countries of West Africa, but little is known on this pathogen. We compared the genomes of 253 Maf clinical isolates from Ghana, including N = 175 Lineage 5 (L5) and N = 78 Lineage 6 (L6). We found that the genomic diversity of L6 was higher than in L5 despite the smaller sample size. Regulatory proteins appeared to evolve neutrally in L5 but under purifying selection in L6. Even though over 90% of the human T cell epitopes were conserved in both lineages, L6 showed a higher ratio of non-synonymous to synonymous single nucleotide variation in these epitopes overall compared to L5. Of the 10% human T cell epitopes that were variable, most carried mutations that were lineage-specific. Our findings indicate that Maf L5 and L6 differ in some of their population genomic characteristics, possibly reflecting different selection pressures linked to distinct ecological niches.

AB - Mycobacterium africanum (Maf) causes a substantial proportion of human tuberculosis in some countries of West Africa, but little is known on this pathogen. We compared the genomes of 253 Maf clinical isolates from Ghana, including N = 175 Lineage 5 (L5) and N = 78 Lineage 6 (L6). We found that the genomic diversity of L6 was higher than in L5 despite the smaller sample size. Regulatory proteins appeared to evolve neutrally in L5 but under purifying selection in L6. Even though over 90% of the human T cell epitopes were conserved in both lineages, L6 showed a higher ratio of non-synonymous to synonymous single nucleotide variation in these epitopes overall compared to L5. Of the 10% human T cell epitopes that were variable, most carried mutations that were lineage-specific. Our findings indicate that Maf L5 and L6 differ in some of their population genomic characteristics, possibly reflecting different selection pressures linked to distinct ecological niches.

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U2 - 10.1038/s41598-018-29620-2

DO - 10.1038/s41598-018-29620-2

M3 - Article

C2 - 30050166

AN - SCOPUS:85050671725

SN - 2045-2322

VL - 8

JO - Scientific Reports

JF - Scientific Reports

IS - 1

M1 - 11269

ER -

Comparative genomics of Mycobacterium africanum Lineage 5 and Lineage 6 from Ghana suggests distinct ecological niches

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