Comparison of Brucella abortus population structure based on genotyping methods with different levels of resolution

Carine R Pereira; Raquel C Neia; Saulo B Silva; Charles H D Williamson; John D Gillece; David O'Callaghan; Jeffrey T Foster; Izabela R C Oliveira; Júlio S S Bueno Filho; Andrey P Lage; Vasco A C Azevedo; Elaine M S Dorneles

doi:10.1016/j.mimet.2023.106772

Comparison of Brucella abortus population structure based on genotyping methods with different levels of resolution

J Microbiol Methods. 2023 Aug:211:106772. doi: 10.1016/j.mimet.2023.106772. Epub 2023 Jun 19.

Affiliations

¹ Faculdade de Zootecnia e Medicina Veterinária, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil.
² Faculdade de Ciências Básicas, Universidade Federal Fluminense, Nova Friburgo, Rio de Janeiro, Brazil.
³ Escola de Ciências da Saúde, Univali, Itajaí, Santa Catarina, Brazil.
⁴ Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.
⁵ Bacterial Virulence and Infectious Disease, University of Montpellier, Nimes, France.
⁶ Departamento de Estatística, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil.
⁷ Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
⁸ Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
⁹ Faculdade de Zootecnia e Medicina Veterinária, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil. Electronic address: elaine.dorneles@ufla.br.

PMID: 37343840
DOI: 10.1016/j.mimet.2023.106772

Abstract

Numerous genotyping techniques based on different principles and with different costs and levels of resolution are currently available for understanding the transmission dynamics of brucellosis worldwide. We aimed to compare the population structure of the genomes of 53 Brazilian Brucella abortus isolates using eight different genotyping methods: multiple-locus variable-number tandem-repeat analysis (MLVA8, MLVA11, MLVA16), multilocus sequence typing (MLST9, MLST21), core genome MLST (cgMLST) and two techniques based on single nucleotide polymorphism (SNP) detection (parSNP and NASP) from whole genomes. The strains were isolated from six different Brazilian states between 1977 and 2008 and had previously been analyzed using MLVA8, MLVA11, and MLVA16. Their whole genomes were sequenced, assembled, and subjected to MLST9 MLST21, cgMLST, and SNP analyses. All the genotypes were compared by hierarchical grouping method based on the average distances between the correlation matrices of each technique. MLST9 and MLST21 had the lowest level of resolution, both revealing only four genotypes. MLVA8, MLVA11, and MLVA16 had progressively increasing levels of resolution as more loci were analyzed, identifying 6, 16, and 44 genotypes, respectively. cgMLST showed the highest level of resolution, identifying 45 genotypes, followed by the SNP-based methods, both of which had 44 genotypes. In the assessed population, MLVA was more discriminatory than MLST and was easier and cheaper to perform. SNP techniques and cgMLST provided the highest levels of resolution and the results from the two methods were in close agreement. In conclusion, the choice of genotyping technique can strongly affect one's ability to make meaningful epidemiological conclusions but is dependent on available resources: while the VNTR based techniques are more indicated to high prevalence scenarios, the WGS methods are the ones with the best discriminative power and therefore recommended for outbreaks investigation.

Keywords: Brucellosis; Epidemiology; MLST; MLVA; SNP; cgMLST.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Brucella abortus* / genetics
Brucellosis* / epidemiology
Genotype
Genotyping Techniques
Humans
Minisatellite Repeats
Multilocus Sequence Typing / methods
Phylogeny