Application of Whole Genome Sequencing and Pan-Family Multi-Locus Sequence Analysis to Characterize Relationships Within the Family Brucellaceae

Abstract

The bacterial family Brucellaceae is currently composed of seven genera, including species of the genus Brucella, a number of which are significant veterinary and zoonotic pathogens. The bacteriological identification of pathogenic Brucella spp. may be hindered by their close phenotypic similarity to other members of the Brucellaceae, particularly of the genus Ochrobactrum. Additionally, a number of novel atypical Brucella taxa have recently been identified, which exhibit greater genetic diversity than observed within the previously described species, and which share genomic features with organisms outside of the genus. Furthermore, previous work has indicated that the genus Ochrobactrum is polyphyletic, raising further questions regarding the relationship between the genus Brucella and wider Brucellaceae. We have applied whole genome sequencing (WGS) and pan-family multi-locus sequence analysis (MLSA) approaches to a comprehensive panel of Brucellaceae type strains, in order to characterize relationships within the family. Phylogenies based on WGS core genome alignments were able to resolve phylogenetic relationships of 31 non-Brucella spp. type strains from within the family, alongside type strains of twelve Brucella species. A phylogeny based on concatenated pan-family MLSA data was largely consistent with WGS based analyses. Notably, recently described atypical Brucella isolates were consistently placed in a single clade with existing species, clearly distinct from all members of the genus Ochrobactrum and wider family. Both WGS and MLSA methods closely grouped Brucella spp. with a subset of Ochrobactrum species. However, results also confirmed that the genus Ochrobactrum is polyphyletic, with seven species forming a separate grouping. The pan-family MLSA scheme was subsequently applied to a panel of 50 field strains of the family Brucellaceae, isolated from a wide variety of sources. This analysis confirmed the utility of the pan-Brucellaceae MLSA scheme in placing field isolates in relation to recognized type strains. However, a significant number of these isolates did not cluster with currently identified type strains, suggesting the existence

Reclassification ofBrucella cicerias later heterotypic synonyms ofBrucella intermedia

“…Besides, the count of features like genomics size and protein count is similar (Figure 1). These observations confirm from the genomic point of view, a previous annotation made by (7,13), in which B. ciceri and B. intermedia could not be discriminated as different species based solely on traits such as 16S ribosomal gene identity, habitat or lifestyle.…”

A Bayesian analysis of a Test and Vaccinate or Remove study to control bovine tuberculosis in badgers (Meles meles)

“…This separation (along with the different independent delivery of the test sample and reagent), may account for the increased DPP test performance over its predecessor both in terms of sensitivity and specificity (BrockTB Stat-Pak test sensitivity estimates 49–58%; specificity estimates 93–97%) [ 38 , 42 , 43 ]. Indeed, these analyses confirm the poor performance of DPP line 2, particularly in relation to specificity, and that only DPP line 1 provided a useful interpretation for bovine TB diagnosis in badgers [ 11 , 44 ].…”

Epidemiology Aspects of Brucella-DNA Detection Using Real-time PCR from Bovine Whole Blood Samples in Colombia

“…Few brucellosis studies have been carried out with spatial analysis involving variables such as proximity to urban and rural areas, altitude, the season of the year, among others (Ibrahim et al, 2010;Dadar et al, 2020), and according to the authors' review, no studies in livestock have evaluated the proximity of herds to main roads. Due to the expansion of the Brucella genus, its evolution, and possible close relationship with environmental bacteria (Ashford et al, 2020), spatial studies are needed to understand the Brucella behaviour in environments.…”