An African origin for Mycobacterium bovis

ABSTRACTBackground and objectivesMycobacterium bovis and Mycobacterium caprae are two of the most important agents of tuberculosis (TB) in livestock and the most important causes of zoonotic TB in humans. However, little is known about the global population structure, phylogeography and evolutionary history of these pathogens.MethodologyWe compiled a global collection of 3364 whole-genome sequences from M. bovis and M. caprae originating from 35 countries and inferred their phylogenetic relationships, geographic origins and age.ResultsOur results resolved the phylogenetic relationship among the four previously defined clonal complexes of M. bovis, and another eight newly described here. Our phylogeographic analysis showed that M. bovis likely originated in East Africa. While some groups remained restricted to East- and West Africa, others have subsequently dispersed to different parts of the world.Conclusions and implicationsOur results allow a better understanding of the global population structure of M. bovis and its evolutionary history. This knowledge can be used to define better molecular markers for epidemiological investigations of M. bovis in settings where whole genome sequencing cannot easily be implemented.

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An African origin for Mycobacterium bovis

Evolution Medicine and Public Health ◽

10.1093/emph/eoaa005 ◽

2020 ◽

Vol 2020 (1) ◽

pp. 49-59 ◽

Cited By ~ 4

Author(s):

Chloé Loiseau ◽

Fabrizio Menardo ◽

Abraham Aseffa ◽

Elena Hailu ◽

Balako Gumi ◽

...

Keyword(s):

Population Structure ◽

West Africa ◽

Mycobacterium Bovis ◽

Evolutionary History ◽

Whole Genome ◽

Genome Sequences ◽

The World ◽

History Of ◽

Global Population ◽

Different Parts

Abstract Background and objectives Mycobacterium bovis and Mycobacterium caprae are two of the most important agents of tuberculosis in livestock and the most important causes of zoonotic tuberculosis in humans. However, little is known about the global population structure, phylogeography and evolutionary history of these pathogens. Methodology We compiled a global collection of 3364 whole-genome sequences from M.bovis and M.caprae originating from 35 countries and inferred their phylogenetic relationships, geographic origins and age. Results Our results resolved the phylogenetic relationship among the four previously defined clonal complexes of M.bovis, and another eight newly described here. Our phylogeographic analysis showed that M.bovis likely originated in East Africa. While some groups remained restricted to East and West Africa, others have subsequently dispersed to different parts of the world. Conclusions and implications Our results allow a better understanding of the global population structure of M.bovis and its evolutionary history. This knowledge can be used to define better molecular markers for epidemiological investigations of M.bovis in settings where whole-genome sequencing cannot easily be implemented. Lay summary During the last few years, analyses of large globally representative collections of whole-genome sequences (WGS) from the human-adapted Mycobacterium tuberculosis complex (MTBC) lineages have enhanced our understanding of the global population structure, phylogeography and evolutionary history of these pathogens. In contrast, little corresponding data exists for M. bovis, the most important agent of tuberculosis in livestock. Using whole-genome sequences of globally distributed M. bovis isolates, we inferred the genetic relationships among different M. bovis genotypes distributed around the world. The most likely origin of M. bovis is East Africa according to our inferences. While some M. bovis groups remained restricted to East and West Africa, others have subsequently dispersed to different parts of the world driven by cattle movements.

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Insights into the evolutionary history of Japanese encephalitis virus (JEV) based on whole-genome sequences comprising the five genotypes

Virology Journal ◽

10.1186/s12985-015-0270-z ◽

2015 ◽

Vol 12 (1) ◽

pp. 43 ◽

Cited By ~ 21

Author(s):

Xiaoyan Gao ◽

Hong Liu ◽

Minghua Li ◽

Shihong Fu ◽

Guodong Liang

Keyword(s):

Japanese Encephalitis Virus ◽

Japanese Encephalitis ◽

Evolutionary History ◽

Encephalitis Virus ◽

Whole Genome ◽

Genome Sequences ◽

History Of

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Dissecting the molecular evolution of fluoroquinolone-resistant Shigella sonnei

Nature Communications ◽

10.1038/s41467-019-12823-0 ◽

2019 ◽

Vol 10 (1) ◽

Cited By ~ 6

Author(s):

Hao Chung The ◽

Christine Boinett ◽

Duy Pham Thanh ◽

Claire Jenkins ◽

Francois-Xavier Weill ◽

...

Keyword(s):

Experimental Evolution ◽

Evolutionary History ◽

Treatment Options ◽

Clonal Expansion ◽

Shigella Sonnei ◽

Whole Genome ◽

Genome Sequences ◽

Complete Resistance ◽

History Of

Abstract Shigella sonnei increasingly dominates the international epidemiological landscape of shigellosis. Treatment options for S. sonnei are dwindling due to resistance to several key antimicrobials, including the fluoroquinolones. Here we analyse nearly 400 S. sonnei whole genome sequences from both endemic and non-endemic regions to delineate the evolutionary history of the recently emergent fluoroquinolone-resistant S. sonnei. We reaffirm that extant resistant organisms belong to a single clonal expansion event. Our results indicate that sequential accumulation of defining mutations (gyrA-S83L, parC-S80I, and gyrA-D87G) led to the emergence of the fluoroquinolone-resistant S. sonnei population around 2007 in South Asia. This clone was then transmitted globally, resulting in establishments in Southeast Asia and Europe. Mutation analysis suggests that the clone became dominant through enhanced adaptation to oxidative stress. Experimental evolution reveals that under fluoroquinolone exposure in vitro, resistant S. sonnei develops further intolerance to the antimicrobial while the susceptible counterpart fails to attain complete resistance.

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Whole Genome Sequencing Refines Knowledge on the Population Structure of Mycobacterium bovis from a Multi-Host Tuberculosis System

Microorganisms ◽

10.3390/microorganisms9081585 ◽

2021 ◽

Vol 9 (8) ◽

pp. 1585

Author(s):

Ana C. Reis ◽

Liliana C. M. Salvador ◽

Suelee Robbe-Austerman ◽

Rogério Tenreiro ◽

Ana Botelho ◽

...

Keyword(s):

Population Structure ◽

Whole Genome Sequencing ◽

Wild Boar ◽

Genome Sequencing ◽

Mycobacterium Bovis ◽

Red Deer ◽

Variable Number Tandem Repeat ◽

Variant Calling ◽

Whole Genome ◽

Network Analyses

Classical molecular analyses of Mycobacterium bovis based on spoligotyping and Variable Number Tandem Repeat (MIRU-VNTR) brought the first insights into the epidemiology of animal tuberculosis (TB) in Portugal, showing high genotypic diversity of circulating strains that mostly cluster within the European 2 clonal complex. Previous surveillance provided valuable information on the prevalence and spatial occurrence of TB and highlighted prevalent genotypes in areas where livestock and wild ungulates are sympatric. However, links at the wildlife–livestock interfaces were established mainly via classical genotype associations. Here, we apply whole genome sequencing (WGS) to cattle, red deer and wild boar isolates to reconstruct the M. bovis population structure in a multi-host, multi-region disease system and to explore links at a fine genomic scale between M. bovis from wildlife hosts and cattle. Whole genome sequences of 44 representative M. bovis isolates, obtained between 2003 and 2015 from three TB hotspots, were compared through single nucleotide polymorphism (SNP) variant calling analyses. Consistent with previous results combining classical genotyping with Bayesian population admixture modelling, SNP-based phylogenies support the branching of this M. bovis population into five genetic clades, three with apparent geographic specificities, as well as the establishment of an SNP catalogue specific to each clade, which may be explored in the future as phylogenetic markers. The core genome alignment of SNPs was integrated within a spatiotemporal metadata framework to further structure this M. bovis population by host species and TB hotspots, providing a baseline for network analyses in different epidemiological and disease control contexts. WGS of M. bovis isolates from Portugal is reported for the first time in this pilot study, refining the spatiotemporal context of TB at the wildlife–livestock interface and providing further support to the key role of red deer and wild boar on disease maintenance. The SNP diversity observed within this dataset supports the natural circulation of M. bovis for a long time period, as well as multiple introduction events of the pathogen in this Iberian multi-host system.

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Population structure and history of the Welsh sheep breeds determined by whole genome genotyping

BMC Genetics ◽

10.1186/s12863-015-0216-x ◽

2015 ◽

Vol 16 (1) ◽

Cited By ~ 32

Author(s):

Sarah E. Beynon ◽

Gancho T. Slavov ◽

Marta Farré ◽

Bolormaa Sunduimijid ◽

Kate Waddams ◽

...

Keyword(s):

Population Structure ◽

Whole Genome ◽

Sheep Breeds ◽

History Of

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Population Structure of Mycobacterium bovis in Germany: a Long-Term Study Using Whole-Genome Sequencing Combined with Conventional Molecular Typing Methods

Journal of Clinical Microbiology ◽

10.1128/jcm.01573-20 ◽

2020 ◽

Vol 58 (11) ◽

Author(s):

Thomas A. Kohl ◽

Katharina Kranzer ◽

Sönke Andres ◽

Thierry Wirth ◽

Stefan Niemann ◽

...

Keyword(s):

Population Structure ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Mycobacterium Bovis ◽

Variable Number Tandem Repeat ◽

Epidemiological Surveillance ◽

Whole Genome ◽

Content Type ◽

Long Term Study ◽

Wide Range

ABSTRACT Mycobacterium bovis is the primary cause of bovine tuberculosis (bTB) and infects a wide range of domestic animal and wildlife species and humans. In Germany, bTB still emerges sporadically in cattle herds, free-ranging wildlife, diverse captive animal species, and humans. In order to understand the underlying population structure and estimate the population size fluctuation through time, we analyzed 131 M. bovis strains from animals (n = 38) and humans (n = 93) in Germany from 1999 to 2017 by whole-genome sequencing (WGS), mycobacterial interspersed repetitive-unit–variable-number tandem-repeat (MIRU-VNTR) typing, and spoligotyping. Based on WGS data analysis, 122 out of the 131 M. bovis strains were classified into 13 major clades, of which 6 contained strains from both human and animal cases and 7 only strains from human cases. Bayesian analyses suggest that the M. bovis population went through two sharp anticlimaxes, one in the middle of the 18th century and another one in the 1950s. WGS-based cluster analysis grouped 46 strains into 13 clusters ranging in size from 2 to 11 members and involving strains from distinct host types, e.g., only cattle and also mixed hosts. Animal strains of four clusters were obtained over a 9-year span, pointing toward autochthonous persistent bTB infection cycles. As expected, WGS had a higher discriminatory power than spoligotyping and MIRU-VNTR typing. In conclusion, our data confirm that WGS and suitable bioinformatics constitute the method of choice to implement prospective molecular epidemiological surveillance of M. bovis. The population of M. bovis in Germany is diverse, with subtle, but existing, interactions between different host groups.

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Culicidae evolutionary history focusing on the Culicinae subfamily based on mitochondrial phylogenomics

Scientific Reports ◽

10.1038/s41598-020-74883-3 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Alexandre Freitas da Silva ◽

Laís Ceschini Machado ◽

Marcia Bicudo de Paula ◽

Carla Júlia da Silva Pessoa Vieira ◽

Roberta Vieira de Morais Bronzoni ◽

...

Keyword(s):

Data Mining ◽

Evolutionary History ◽

Mosquito Species ◽

Whole Genome ◽

Lack Of Information ◽

Fundamental Information ◽

History Of ◽

Medical Importance ◽

Low Coverage

Abstract Mosquitoes are insects of medical importance due their role as vectors of different pathogens to humans. There is a lack of information about the evolutionary history and phylogenetic positioning of the majority of mosquito species. Here we characterized the mitogenomes of mosquito species through low-coverage whole genome sequencing and data mining. A total of 37 draft mitogenomes of different species were assembled from which 16 are newly-sequenced species. We datamined additional 49 mosquito mitogenomes, and together with our 37 mitogenomes, we reconstructed the evolutionary history of 86 species including representatives from 15 genera and 7 tribes. Our results showed that most of the species clustered in clades with other members of their own genus with exception of Aedes genus which was paraphyletic. We confirmed the monophyletic status of the Mansoniini tribe including both Coquillettidia and Mansonia genus. The Aedeomyiini and Uranotaeniini were consistently recovered as basal to other tribes in the subfamily Culicinae, although the exact relationships among these tribes differed between analyses. These results demonstrate that low-coverage sequencing is effective to recover mitogenomes, establish phylogenetic knowledge and hence generate basic fundamental information that will help in the understanding of the role of these species as pathogen vectors.

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Global Population Structure and Natural History of the Green Turtle (Chelonia mydas) in Terms of Matriarchal Phylogeny

Evolution ◽

10.2307/2409742 ◽

1992 ◽

Vol 46 (4) ◽

pp. 865 ◽

Cited By ~ 107

Author(s):

Brian W. Bowen ◽

Anne B. Meylan ◽

J. Perran Ross ◽

Colin J. Limpus ◽

George H. Balazs ◽

...

Keyword(s):

Population Structure ◽

Natural History ◽

Green Turtle ◽

Chelonia Mydas ◽

History Of ◽

Global Population

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The origin, current diversity and future conservation of the modern lion ( Panthera leo )

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2006.3555 ◽

2006 ◽

Vol 273 (1598) ◽

pp. 2119-2125 ◽

Cited By ~ 60

Author(s):

Ross Barnett ◽

Nobuyuki Yamaguchi ◽

Ian Barnes ◽

Alan Cooper

Keyword(s):

Evolutionary History ◽

Mitochondrial Control Region ◽

Modern Human ◽

Conservation Strategies ◽

African Origin ◽

Continental Scale ◽

History Of ◽

Physical Barriers ◽

Geographic Populations ◽

Sub Saharan

Understanding the phylogeographic processes affecting endangered species is crucial both to interpreting their evolutionary history and to the establishment of conservation strategies. Lions provide a key opportunity to explore such processes; however, a lack of genetic diversity and shortage of suitable samples has until now hindered such investigation. We used mitochondrial control region DNA (mtDNA) sequences to investigate the phylogeographic history of modern lions, using samples from across their entire range. We find the sub-Saharan African lions are basal among modern lions, supporting a single African origin model of modern lion evolution, equivalent to the ‘recent African origin’ model of modern human evolution. We also find the greatest variety of mtDNA haplotypes in the centre of Africa, which may be due to the distribution of physical barriers and continental-scale habitat changes caused by Pleistocene glacial oscillations. Our results suggest that the modern lion may currently consist of three geographic populations on the basis of their recent evolutionary history: North African–Asian, southern African and middle African. Future conservation strategies should take these evolutionary subdivisions into consideration.

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