New insights into phylogeography of worldwide  Brucella canis  isolates by comparative genomics-based approaches: focus on Brazil

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Abstract

Background

Canine brucellosis, due to Brucella canis, is a worldwide zoonosis that remains endemic in South America, including Brazil. Implementation of powerful whole-genome sequencing approaches allowed exploring the Brucella genus considered as monomorphic, with, to date, more than 500 genomes available in public databases . Nevertheless, with under-representation of B. canis genomes −only twenty complete or draft genomes−, lack of knowledge about this species is still considerable. This report describes a comparative genomics-based phylogeographic investigation of 53 B. canis strains, including 28 isolates paired-end sequenced in this work.

Results

Obtained results allow identifying a SNP panel species-specific to B. canis of 1086 nucleotides. In addition, high-resolution analyses assess the epidemiological relationship between worldwide isolates. Our findings show worldwide strains are distributed among 2 distinct lineages. One of them seems to be specific to South American strains, including Brazil. B. canis South American strains may be identified by a SNP panel of 15 nucleotides, whereas a 22 SNP panel is sufficient to define contamination origin from Brazil. These results lead to the proposal of a possible spread route for dog brucellosis through South America. Additionally, whole-genome analyses highlight the remarkable genomic stability of B. canis strains over time and the sustainability of the infection in São Paulo over 12 year-period.

Conclusions

Significant increase of B. canis genomes available in public databases provides new insights into B. canis infection in South America, including Brazil, as well as in the world, and also offers new perspectives for the Brucella genus largo sensu.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5001-6) contains supplementary material, which is available to authorized users.

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Most cited references 22

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ART: a next-generation sequencing read simulator.

Weichun Huang, Leping Li, Jason R. Myers … (2012)

ART is a set of simulation tools that generate synthetic next-generation sequencing reads. This functionality is essential for testing and benchmarking tools for next-generation sequencing data analysis including read alignment, de novo assembly and genetic variation discovery. ART generates simulated sequencing reads by emulating the sequencing process with built-in, technology-specific read error models and base quality value profiles parameterized empirically in large sequencing datasets. We currently support all three major commercial next-generation sequencing platforms: Roche's 454, Illumina's Solexa and Applied Biosystems' SOLiD. ART also allows the flexibility to use customized read error model parameters and quality profiles. Both source and binary software packages are available at http://www.niehs.nih.gov/research/resources/software/art.

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Evaluation and selection of tandem repeat loci for a Brucella MLVA typing assay

Philippe Le Flèche, Isabelle Jacques, Maggy Grayon … (2006)

Background The classification of Brucella into species and biovars relies on phenotypic characteristics and sometimes raises difficulties in the interpretation of the results due to an absence of standardization of the typing reagents. In addition, the resolution of this biotyping is moderate and requires the manipulation of the living agent. More efficient DNA-based methods are needed, and this work explores the suitability of multiple locus variable number tandem repeats analysis (MLVA) for both typing and species identification. Results Eighty tandem repeat loci predicted to be polymorphic by genome sequence analysis of three available Brucella genome sequences were tested for polymorphism by genotyping 21 Brucella strains (18 reference strains representing the six 'classical' species and all biovars as well as 3 marine mammal strains currently recognized as members of two new species). The MLVA data efficiently cluster the strains as expected according to their species and biovar. For practical use, a subset of 15 loci preserving this clustering was selected and applied to the typing of 236 isolates. Using this MLVA-15 assay, the clusters generated correspond to the classical biotyping scheme of Brucella spp. The 15 markers have been divided into two groups, one comprising 8 user-friendly minisatellite markers with a good species identification capability (panel 1) and another complementary group of 7 microsatellite markers with higher discriminatory power (panel 2). Conclusion The MLVA-15 assay can be applied to large collections of Brucella strains with automated or manual procedures, and can be proposed as a complement, or even a substitute, of classical biotyping methods. This is facilitated by the fact that MLVA is based on non-infectious material (DNA) whereas the biotyping procedure itself requires the manipulation of the living agent. The data produced can be queried on a dedicated MLVA web service site.

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Characterisation of the genetic diversity of Brucella by multilocus sequencing

Adrian M Whatmore, Lorraine Perrett, Alastair MacMillan (2007)

Background Brucella species include economically important zoonotic pathogens that can infect a wide range of animals. There are currently six classically recognised species of Brucella although, as yet unnamed, isolates from various marine mammal species have been reported. In order to investigate genetic relationships within the group and identify potential diagnostic markers we have sequenced multiple genetic loci from a large sample of Brucella isolates representing the known diversity of the genus. Results Nine discrete genomic loci corresponding to 4,396 bp of sequence were examined from 160 Brucella isolates. By assigning each distinct allele at a locus an arbitrary numerical designation the population was found to represent 27 distinct sequence types (STs). Diversity at each locus ranged from 1.03–2.45% while overall genetic diversity equated to 1.5%. Most loci examined represent housekeeping gene loci and, in all but one case, the ratio of non-synonymous to synonymous change was substantially <1. Analysis of linkage equilibrium between loci indicated a strongly clonal overall population structure. Concatenated sequence data were used to construct an unrooted neighbour-joining tree representing the relationships between STs. This shows that four previously characterized classical Brucella species, B. abortus, B. melitensis, B. ovis and B. neotomae correspond to well-separated clusters. With the exception of biovar 5, B. suis isolates cluster together, although they form a more diverse group than other classical species with a number of distinct STs corresponding to the remaining four biovars. B. canis isolates are located on the same branch very closely related to, but distinguishable from, B. suis biovar 3 and 4 isolates. Marine mammal isolates represent a distinct, though rather weakly supported, cluster within which individual STs display one of three clear host preferences. Conclusion The sequence database provides a powerful dataset for addressing ongoing controversies in Brucella taxonomy and a tool for unambiguously placing atypical, phenotypically discordant or newly emerging Brucella isolates. Furthermore, by using the phylogenetic backbone described here, robust and rationally selected markers for use in diagnostic assay development can be identified.

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Author and article information

Contributors

Acácia Ferreira Vicente: acacia.ferreiravicente@anses.fr

Guillaume Girault: guillaume.girault@anses.fr

Yannick Corde: yannick.corde@neuf.fr

Mateus Souza Ribeiro Mioni: mateusmioni@yahoo.com.br

Lara Borges Keid: larakeid@usp.br

Maryne Jay: maryne.jay@anses.fr

Jane Megid: jane@fmvz.unesp.br

Virginie Mick: virginie.mick@anses.fr

Journal

Journal ID (nlm-ta): BMC Genomics

Journal ID (iso-abbrev): BMC Genomics

Title: BMC Genomics

Publisher: BioMed Central (London )

ISSN (Electronic): 1471-2164

Publication date (Electronic): 28 August 2018

Publication date PMC-release: 28 August 2018

Publication date Collection: 2018

Volume: 19

Electronic Location Identifier: 636

Affiliations

[1 ]EU/OIE/FAO & National Reference Laboratory for animal Brucellosis, Animal Health Laboratory, Paris-Est University/Anses, Maisons-Alfort, France

[2 ]ISNI 0000 0001 2188 478X, GRID grid.410543.7, Molecular Biology Laboratory, Dept. Veterinary Hygiene and Public Health, , FMVZ, UNESP, ; Botucatu, Brazil

[3 ]ISNI 0000 0004 1937 0722, GRID grid.11899.38, Dept. Veterinary Medicine, , University of Animal Science and Food Engineering, USP, ; Pirassununga, Brazil

[4 ]GRID grid.418065.e, Present Address: Physiology of reproduction and behaviour joint research unit, INRA Val de Loire Centre, ; Nouzilly, France

[5 ]ISNI 0000 0001 2153 9484, GRID grid.434200.1, Present Address: Anses, Laboratoire de Lyon, UMR Mycoplasmoses des Ruminants, Lyon, France Université de Lyon, VetAgro Sup, UMR Mycoplasmoses des Ruminants, ; Marcy L’Etoile, France

Article

Publisher ID: 5001

DOI: 10.1186/s12864-018-5001-6

PMC ID: 6114238

PubMed ID: 30153798

SO-VID: 32d46fb4-ad04-46df-8a1d-78b72179484e

License:

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

History

Date received : 24 January 2018

Date accepted : 8 August 2018

Funding

Funded by: FAPESP

Award ID: 2014/00889-0

Funded by: CAPES

Award ID: 88887.117958/2016-00

Funded by: Bru-EPIDIA

Award ID: 291815-FP7/ERANET/ ANIHWA

Custom metadata

ScienceOpen disciplines: Genetics

Keywords: brucella canis,dog brucellosis,brazil,são paulo,europe,whole genome sequencing,snp,phylogeography

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ScienceOpen disciplines: Genetics

Keywords: brucella canis, dog brucellosis, brazil, são paulo, europe, whole genome sequencing, snp, phylogeography

New insights into phylogeography of worldwide Brucella canis isolates by comparative genomics-based approaches: focus on Brazil

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Electronic supplementary material

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SciELO Brazil

Most cited references 22

ART: a next-generation sequencing read simulator.

Evaluation and selection of tandem repeat loci for a Brucella MLVA typing assay

Characterisation of the genetic diversity of Brucella by multilocus sequencing

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