Tracking the Distribution of Brucella abortus in Egypt Based on Core Genome SNP Analysis and In Silico MLVA-16

Abstract

Brucellosis, caused by the bacteria of the genus Brucella, is one of the most neglected common zoonotic diseases globally with a public health significance and a high economic loss among the livestock industry worldwide. Since little is known about the distribution of B. abortus in Egypt, a total of 46 B. abortus isolates recovered between 2012–2020, plus one animal isolate from 2006, were analyzed by examining the whole core genome single nucleotide polymorphism (cgSNP) in comparison to the in silico multilocus variable number of tandem repeat analysis (MLVA). Both cgSNP analysis and MLVA revealed three clusters and one isolate only was distantly related to the others. One cluster identified a rather widely distributed outbreak strain which is repeatedly occurring for at least 16 years with marginal deviations in cgSNP analysis. The other cluster of isolates represents a rather newly introduced outbreak strain. A separate cluster comprised RB51 vaccine related strains, isolated from aborted material. The comparison with MLVA data sets from public databases reveals one near relative from Argentina to the oldest outbreak strain and a related strain from Spain to a newly introduced outbreak strain in Egypt. The distantly related isolate matches with a strain from Portugal in the MLVA profile. Based on cgSNP analysis the oldest outbreak strain clusters with strains from the UK. Compared to the in silico analysis of MLVA, cgSNP analysis using WGS data provides a much higher resolution of genotypes and, when correlated to the associated epidemiological metadata, cgSNP analysis allows the differentiation of outbreaks by defining different outbreak strains. In this respect, MLVA data are error-prone and can lead to incorrect interpretations of outbreak events.

Sequence-based detection and typing procedures for Burkholderia mallei: Assessment and prospects

“…While this is commonly done for some pathogens, such as Brucella sp. ( 57 ), this approach has limitations for other bacteria such as Bacillus anthracis ( 58 ) and also B. mallei ( 59 ). Indeed, MLVA profiles obtained in silico from genomes of Pakistani B. mallei strains differed markedly from previously published profiles, disqualifying this in silico approach from sequencing data obtained by Illumina technology.…”

“…This high-resolution typing is required for unambiguous attribution of infection sources, infection chains and tracing of pathogens as sequences types of different strains can be assessed, provided that sufficient isolates and information is available. Thus, in silico analysis might completely substitute classical PCR-based approaches in the future ( 56 ), as MLVA and MLST-7 could be conducted based on the genome sequence ( 57 , 74 ). Whether this is applicable to B. mallei has to be carefully assessed yet, as the construction of highly accurate genomes is a prerequisite for the application of these methods.…”

Whole-genome sequencing for genetic diversity analysis of Iranian Brucella spp. isolated from humans and livestock

“…Whole genome sequencing-based typing methods provide the discriminatory power to differentiate closely related strains [ 23 , 51 ]. Using in silico analysis, three MLST types of B. melitensis were identified with the most common being ST8 ( n = 26) isolated from a wide variety of host species.…”

“…[ 18 ]. Therefore, different genetic tools such as whole genome sequencing (WGS) have to be employed to trace the geographic origin of isolates and their phylogenetic connection [ [19] , [20] , [21] , [22] , [23] ]. Multiple Locus Variable Number Tandem Repeat (VNTR) Analysis (MLVA) has been introduced as a valuable PCR-based molecular typing approach with high discriminatory power to differentiate Brucella isolates in epidemiological investigations [ [24] , [25] , [26] , [27] ].…”

Editorial: The Transition Era to New Sequencing Technologies and Their Application to Integrative Omics in Molecular Surveillance

“…Via pangenome analysis and MLST, the authors were able to predict several virulence genes and prophage regions and they were able to phylogenetically resolve different lineages of this species within India, where many isolates have been previously reported. The decreasing costs of NGS, open-source bioinformatics tools, and more easily operated laboratory technology make this approach more globally accessible for monitoring ( Holzer et al, 2021 ; Khan et al, 2021 ). In another study, Parra-Flores et al were able to give a detailed profile of virulence and antimicrobial resistance (AMR) proteins of Cronobacter sakazakii strains by adding MALDI-TOF-MS data to WGS data.…”