MLVA-16 analysis
MLVA-16 including Panel 1 (bruce06, bruce08, bruce11, bruce12, bruce42,
bruce43, bruce45, and bruce55) and 8 microsatellite markers including
panel 2A (bruce18, bruce19, and bruce21), and panel 2B (bruce04,
bruce07, bruce09, bruce16, and bruce30) (Le Fleche et al., 2006;
Al Dahouk et al. , 2007) were performed for the B.
melitensis bv3 isolates (n=41). In phylogeny, dendrograms were
performed after uploading the VNTRs data and estimating theBrucella genotypes online through the MLVA bank for microbe
genotyping
(http://microbesgenotyping.i2bc.paris-saclay.fr).
Dendrograms seeking the genetic similarities among the 41Brucella strains were based on the categorical coefficient with
distance calculation and unweighted pair group method with arithmetic
mean (UPGMA) using BioNumerics version 7.6 (Applied Maths, Belgium).
VNTRs data of the local B. melitensis strains used in this study
were compared with 118 B. melitensis strains recovered from
different animal species and humans from other Egyptian governorates
(Sayour et al. 2020). The standard minimum spanning tree (MST), based on
categorical coefficient with double locus variance priority rules as
well as the dendrogram of the supplementary file 1, was used to study
the genetic similarities between the local strains along with the
MLVA-16 global metadata of the B. melitensis bv3 strains (n=358)
isolated from selected African countries (neighborhood) and worldwide.
The genetic diversity of each MLVA-16 loci was estimated using the HGDI
with 95% confidence intervals through the V-DICE tool available at the
HPA website
(http://www.hpa-bioinformatics.org.uk/cgi-bin/DICI/DICI.pl) where
it ranged from 0 (identical strains) to 1 (different strains) as
reported by Hunter and Gaston (1988). Sola et al. (2003) have classified
the allelic diversity (HGDI) as high if the discriminatory power of HGDI
is more than 0.6, moderate discrimination if 0.3 ≤ HGDI≤0.6, and poor
discrimination if HGDI < 0.3.