Original scientific paper

https://doi.org/10.46419/vs.53.1.9

Efficacy of next-generation sequencing in bacterial zoonoses diagnostics

Sanja Duvnjak ; Croatian Veterinary Institute, Zagreb, Croatia
Željko Pavlinec orcid.org/0000-0001-7128-4280 ; Croatian Veterinary Institute, Zagreb, Croatia
Robert Vaser ; Faculty of Electrical Engineering and Computing, Zagreb, Croatia
Krešimir Križanović ; Faculty of Electrical Engineering and Computing, Zagreb, Croatia
Mile Šikić ; Genome institute Singapore, A*STAR, 60 Biopolis St, Singapore
Maja Zdelar-Tuk orcid.org/0000-0002-9349-6177 ; Croatian Veterinary Institute, Zagreb, Croatia
Irena Reil orcid.org/0000-0002-2198-557X ; Croatian Veterinary Institute, Zagreb, Croatia
Silvio Špičić orcid.org/0000-0001-8317-5831 ; Croatian Veterinary Institute, Zagreb, Croatia

Abstract

Brucella, an extremely diverse but yet genetically highly homogenous genus of bacteria, has been a puzzle for scientists for many decades. These bacteria remain a prominent public health issue, particularly in the Balkan region. Correctly identifying and understanding the pathogen is a vital step in the epidemiology and epizootiology of any bacteria. Identification can be challenging, especially in the case of zoonotic species. This study aimed to implement fourth-generation sequencing in the typing of 11 Brucella suis strains kept in our archive and to compare this method to the classical and non-sequencing based molecular methods used to date. Classical biotyping is highly subjective and gave inconclusive results for 3 strains. Molecular methods used were multiplex PCR and RFLP methods since no one method can identify both species and biovar which is vital in the case of Brucella suis infections. Species and biovars of all the strains were successfully confirmed and in concordance with biotyping results. Oxford Nanopore long-read sequencing was used on a MinION device for next-generation sequencing (NGS). Various algorithms were implemented for genome assembly and BioNumerics 8.0 software was used for MLST identification and analysis. MLST 21 was used for biovar identification and epidemiological comparison of tested strains. The assembled genomes were 3,2 Mb in size and assembled into two chromosomes. MLST 21 analysis placed our strains into species and biovar clusters in concordance with other molecular tests used. To the extent of our knowledge, this is the first documented use of long-read sequencing in Brucella suis identification in this region. We conclude that bacteriological biotyping is outdated and host-specific identification in this genus is incorrect and that molecular characterisation is always the safer, faster and more suitable option. MinION sequencing proved to be a strong, accessible solution for species determination. Future study is required to determine how detailed genome information it can give, considering the error rate.

Keywords

Brucella suis; brucellosis; swine; horses; Nanopore MinION; NGS

Hrčak ID:

261506

URI

https://hrcak.srce.hr/261506

Publication date:

17.6.2021.

Article data in other languages: croatian

Visits: 2.183 *