The Nature and Evolution of Genomic Diversity in the Mycobacterium tuberculosis Complex

Brites, Daniela; Gagneux, Sébastien

doi:10.1007/978-3-319-64371-7_1

Cited by 59 publications

(55 citation statements)

References 142 publications

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“…Moreover, bovine TB is responsible for high economic losses in livestock production globally ( Waters et al, 2012 ) and represents an ongoing threat for zoonotic TB in humans ( Olea-Popelka et al, 2017 ). The causative agents of TB in humans and animals are a group of closely related acid-fast bacilli collectively known as the Mycobacterium tuberculosis complex (MTBC) ( Brites and Gagneux, 2017 ; Malone and Gordon, 2017 ). The human-adapted MTBC comprises five main phylogenetic lineages generally referred to as Mycobacterium tuberculosis sensu stricto (i.e., MTBC lineages 1–4 and lineage 7) and two lineages traditionally known as Mycobacterium africanum (i.e., MTBC lineages 5 and 6) ( de Jong et al, 2010 ; Brites and Gagneux, 2017 ; Yeboah-Manu et al, 2017 ).…”

Section: Introductionmentioning

confidence: 99%

A New Phylogenetic Framework for the Animal-Adapted Mycobacterium tuberculosis Complex

et al. 2018

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Tuberculosis (TB) affects humans and other animals and is caused by bacteria from the Mycobacterium tuberculosis complex (MTBC). Previous studies have shown that there are at least nine members of the MTBC infecting animals other than humans; these have also been referred to as ecotypes. However, the ecology and the evolution of these animal-adapted MTBC ecotypes are poorly understood. Here we screened 12,886 publicly available MTBC genomes and newly sequenced 17 animal-adapted MTBC strains, gathering a total of 529 genomes of animal-adapted MTBC strains. Phylogenomic and comparative analyses confirm that the animal-adapted MTBC members are paraphyletic with some members more closely related to the human-adapted Mycobacterium africanum Lineage 6 than to other animal-adapted strains. Furthermore, we identified four main animal-adapted MTBC clades that might correspond to four main host shifts; two of these clades are hypothesized to reflect independent cattle domestication events. Contrary to what would be expected from an obligate pathogen, MTBC nucleotide diversity was not positively correlated with host phylogenetic distances, suggesting that host tropism in the animal-adapted MTBC seems to be driven by contact rates and demographic aspects of the host population rather by than host relatedness. By combining phylogenomics with ecological data, we propose an evolutionary scenario in which the ancestor of Lineage 6 and all animal-adapted MTBC ecotypes was a generalist pathogen that subsequently adapted to different host species. This study provides a new phylogenetic framework to better understand the evolution of the different ecotypes of the MTBC and guide future work aimed at elucidating the molecular mechanisms underlying host range.

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Section: Introductionmentioning

confidence: 99%

A New Phylogenetic Framework for the Animal-Adapted Mycobacterium tuberculosis Complex

et al. 2018

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“…Based on previous studies performed in the same geographical region, lineage 4 was expected to be most prevalent in pulmonary TB (25), and lineage 2 was expected to be most prevalent in children with TBM (6). However, additional studies show an equal distribution of lineages 2 and 4 for both pulmonary and extrapulmonary TB (3,13).…”

Section: Discussionmentioning

confidence: 94%

Bacterial Genotyping of Central Nervous System Tuberculosis in South Africa: Heterogenic Mycobacterium tuberculosis Infection and Predominance of Lineage 4

et al. 2019

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Tuberculous meningitis (TBM), the most severe extrapulmonary manifestation of tuberculosis, is caused by the pathogen Mycobacterium tuberculosis. The M. tuberculosis complex includes seven lineages, all described to harbor a unique geographical dissemination pattern and clinical presentation. In this study, we set out to determine whether a certain M. tuberculosis lineage demonstrated tropism to cause TBM in patients from Cape Town, South Africa. DNA was extracted from formalin-fixed paraffin-embedded central nervous system (CNS) tissue from a unique neuropathological cohort of 83 TBM patients, collected between 1975 and 2012. M. tuberculosis lineages 1, 2, 3, and 4 were determined using an allele-specific PCR and Sanger sequencing. Of the 83 patient specimens tested, bacterial characterization could be performed on 46 specimens (55%). M. tuberculosis lineage 4 was present in 26 patient specimens (56%), and non-lineage 4 was identified in 10 cases (22%). Moreover, genomic heterogeneity was detected in the CNS specimens of 7 adults and 3 children. We could show that infection of the CNS is not restricted to a single M. tuberculosis lineage and that even young children with rapid progression of disease can harbor more than one M. tuberculosis lineage in the CNS.

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“…Host genetic diversity or pathogen-host co-evolution have been considered as critical factors affecting pathogen genetic diversity in a number of studies (23)(24)(25)(26)(27)(28). Accordingly, the host macaque species and host genetic diversity could be important factors affecting E. nuttalli genetic diversity.…”

Section: Discussionmentioning

confidence: 99%

Correlation of genetic diversity between hosts and parasites in <i>Entamoeba nuttalli</i> isolates from Tibetan and rhesus macaques in China

Miao

Feng

Guan

et al. 2018

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Entamoeba nuttalli infection is prevalent in captive and wild macaques. Recent studies have suggested that genotypes of E. nuttalli isolates are correlated with the geographical distribution of host macaques. Correlation of amoebic genotypes with genetic diversity of host macaques was analyzed in present study. Sixty fresh stool samples were obtained from wild Tibetan macaques living in Mount Huang (HS) of the An-hui Province in China. PCR analysis revealed that the most prevalent Entamoeba species was E. chattoni (E. polecki ST2) (86.7%) followed by E. nuttalli (58.3%) and E. coli (25%). Six E. nuttalli HS isolates were successfully cultured. The tRNA-linked short tandem repeat (STR) loci and serine-rich protein gene of E. nuttalli isolates from four different regions of China (Mount Long-hu, Gui-yang, Mount E-mei, and HS, the former three isolates were obtained in previous studies) were studied and high numbers of polymorphisms were detected. When genetic diversity of different populations of E. nuttalli isolates was compared with geographical distance, an r value of 0.919 was assigned by a Mantel test based on the tRNA-STR loci. In host macaques, the mtDNA HVS-I gene was also highly polymorphic in each of the genomes. Multiple regression analysis using E. nuttalli tRNA-STR loci genetic, macaque mtDNA HVS-I gene, and geographic distances showed an r value of 0.943, indicating that a higher relevance was demonstrated when geographic and host gene factors were considered. Analysis of genetic factor of host would benefit for better understanding of the evolution of E. nuttalli.

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The Nature and Evolution of Genomic Diversity in the Mycobacterium tuberculosis Complex

Cited by 59 publications

References 142 publications

A New Phylogenetic Framework for the Animal-Adapted Mycobacterium tuberculosis Complex

A New Phylogenetic Framework for the Animal-Adapted Mycobacterium tuberculosis Complex

Bacterial Genotyping of Central Nervous System Tuberculosis in South Africa: Heterogenic Mycobacterium tuberculosis Infection and Predominance of Lineage 4

Correlation of genetic diversity between hosts and parasites in <i>Entamoeba nuttalli</i> isolates from Tibetan and rhesus macaques in China

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