Abstract
Brucellosis is an important zoonosis that is emerging in some regions of the world, gaining increased relevance with the inclusion of the causing agent Brucella spp. in the class B bioterrorism group. Until now, multi-locus VNTR Analysis (MLVA) based on 16 loci has been considered as the gold standard for Brucella typing. However, this methodology is laborious, and, with the rampant release of Brucella genomes, the transition from the traditional MLVA to whole genome sequencing (WGS)-based typing is on course. Nevertheless, in order to avoid a disruptive transition with the loss of massive genetic data obtained throughout the last decade and considering that the transition timings will vary considerably among different countries, it is important to determine WGS-based MLVA alleles of the nowadays sequenced genomes. On this regard, we aimed to evaluate the performance of a Python script that had been previously developed for the rapid in silico extraction of the MLVA alleles, by comparing it to the PCR-based MLVA procedure over 83 strains from different Brucella species. The WGS-based MLVA approach detected 95.3% of all possible 1,328 hits (83 strains×16 loci) and showed an agreement rate with the PCR-based MLVA procedure of 96.4% for MLVA-16. According to our dataset, we suggest the use of a minimal depth of coverage of ~50x and a maximum number of ~200 contigs as guiding “boundaries” for the future application of the script. In conclusion, the evaluated script seems to be a very useful and robust tool for the in silico determination of MLVA profiles of Brucella strains, allowing retrospective and prospective molecular epidemiological studies, which are important for maintaining an active epidemiological surveillance of brucellosis.
Highlights
Brucellosis is one of the most common bacterial zoonosis causing great damage to the farming industry and public health (Franc et al, 2018)
As no experimental validation of such script was performed, we aimed to evaluate the agreement among the multi-locus Variable Number Tandem Repeats (VNTR) Analysis (MLVA) profiles determined through PCR- and whole genome sequencing (WGS)-based approaches for strains from several Brucella species, in order to check the validity of such technological transition underlying the genetic characterization of Brucella
The performance of the WGS-based MLVA approach was assessed through the determination of the percentage of agreement with the results obtained by using the gold standard PCR-based MLVA
Summary
Brucellosis is one of the most common bacterial zoonosis causing great damage to the farming industry and public health (Franc et al, 2018). The brucellosis burden on low-income countries has led the World Health Organization (WHO) to classify it as one of the world’s leading neglected zoonotic diseases (WHO, 2020). Brucellosis is transmitted to humans by ingestion of unpasteurized dairy products or by direct contact with infected animals, placentas, or aborted fetuses (Young, 2005). It can constitute a severely debilitating illness, with diverse symptoms ranging from fever, sweating, fatigue, weight loss, headache, and joint pain. Neurological complications, such as personality changes, meningitides, encephalitis, and peripheral neuropathy, can occur (Dean et al, 2012)
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