Molecular characteristics of Brucella melitensis isolates from humans in Qinghai Province, China

Abstract Background The prevalence of human brucellosis in Qinghai Province of China has been increasing rapidly, with confirmed cases distributed across 31 counties. However, the epidemiology of brucellosis transmission has not been fully elucidated. To characterize the infecting strains isolated from humans, multiple-locus variable-number tandem repeats analysis (MLVA) and whole-genome single-nucleotide polymorphism (SNP)-based approaches were employed. Methods Strains were isolated from two males blood cultures that were confirmed Brucella melitensis positive following biotyping and MLVA. Genomic DNA was extracted from these two strains, and whole-genome sequencing was performed. Next, SNP-based phylogenetic analysis was performed to compare the two strains to 94 B. melitensis strains (complete genome and draft genome) retrieved from online databases. Results The two Brucella isolates were identified as B. melitensis biovar 3 (QH2019001 and QH2019005) following conventional biotyping and were found to have differences in their variable number tandem repeats (VNTRs) using MLVA-16. Phylogenetic examination assigned the 96 strains to five genotype groups, with QH2019001 and QH2019005 assigned to the same group, but different subgroups. Moreover, the QH2019005 strain was assigned to a new subgenotype, IIj, within genotype II. These findings were then combined to determine the geographic origin of the two Brucella strains. Conclusions Utilizing a whole-genome SNP-based approach enabled differences between the two B. melitensis strains to be more clearly resolved, and facilitated the elucidation of their different evolutionary histories. This approach also revealed that QH2019005 is a member of a new subgenotype (IIj) with an ancient origin in the eastern Mediterranean Sea.

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Molecular characteristics of Brucella melitensis isolates from humans in Qinghai Province, China

10.21203/rs.3.rs-81442/v1 ◽

2020 ◽

Author(s):

Zhijun Zhao ◽

Jiquan Li ◽

Li Ma ◽

Hongmei Xue ◽

Xuxin Yang ◽

...

Keyword(s):

Tandem Repeats ◽

Brucella Melitensis ◽

Draft Genome ◽

Geographic Origin ◽

Variable Number ◽

Human Brucellosis ◽

Molecular Characteristics ◽

Whole Genome ◽

Qinghai Province ◽

Variable Number Tandem Repeats

Abstract Background The prevalence of human brucellosis in Qinghai Province has been increasing rapidly, with confirmed cases distributed across 31 counties. However, the epidemiology of brucellosis transmission has not been fully elucidated. To characterize the two isolated strains, multiple locus variable-number tandem repeats analysis (MLVA) and whole-genome single-nucleotide polymorphism (SNP)-based approaches were employed. Methods Blood samples were isolated from two males that were confirmed B. melitensis positive following MLVA. Genomic DNA was extracted from these samples, and whole-genome sequencing (WGS) was performed. Next, SNP-based phylogenetic analysis was performed to compare the two strains to 94 B. melitensis strains (complete genome and draft genome) retrieved from online databases. Results The two Brucella isolates were identified as B. melitensis biovar 3 (QH2019001 and QH2019005) following conventional biotyping and were found to have differences in their variable number tandem repeats (VNTRs) using MLVA-16. Phylogenetic examination assigned the 96 strains to five genotype groups, with QH2019001 and QH2019005 assigned to the same group, but different subgroups. Moreover, the QH2019005 strain was assigned to a new subgenotype, IIj, within genotype II. These findings were then combined to determine the geographic origin of the two Brucella strains. Conclusions Utilizing a whole-genome SNP-based approach enabled differences between the two B. melitensis strains to be more clearly resolved, and facilitated the elucidation of their different evolutionary histories. This approach also revealed that QH2019005 is a member of a new subgenotype (IIj) with an ancient origin in the eastern Mediterranean Sea.

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Whole Genome Sequencing for Tracing Geographical Origin of Imported Cases of Human Brucellosis in Sweden

Microorganisms ◽

10.3390/microorganisms7100398 ◽

2019 ◽

Vol 7 (10) ◽

pp. 398 ◽

Cited By ~ 4

Author(s):

Sacchini ◽

Wahab ◽

Di Giannatale ◽

Zilli ◽

Abass ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Tandem Repeats ◽

Brucella Melitensis ◽

Geographic Origin ◽

Variable Number ◽

Human Brucellosis ◽

Whole Genome ◽

Multiple Loci ◽

Imported Cases

Human infections with Brucella melitensis are occasionally reported in Sweden, despite the fact that the national flocks of sheep and goats are officially free from brucellosis. The aim of our study was to analyze 103 isolates of B. melitensis collected from patients in Sweden between 1994 and 2016 and determine their putative geographic origin using whole genome sequencing (WGS)-based tools. The majority of the strains were assigned to East Mediterranean and African lineages. Both in silico Multiple Loci VNTR (Variable Number of Tandem Repeats) Analysis (MLVA) and core genome Multilocus Sequence Typing (cgMLST) analyses identified countries of the Middle East as the most probable source of origin of the majority of the strains. Isolates collected from patients with travel history to Iraq or Syria were often associated with genotypes from Turkey, as the cgMLST profiles from these countries clustered together. Sixty strains were located within a distance of 20 core genes to related genotypes from the publicly available database, and for eighteen isolates, the closest genotype was different by more than 50 loci. Our study showed that WGS based tools are effective in tracing back the geographic origin of infection of patients with unknown travel status, provided that public sequences from the location of the source are available.

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Genome Sequences of Brucella Melitensis Strains QH2019001 and QH2019005 Provides Insight Into Different Evolutionary Origins Within Qinghai Province, China

10.21203/rs.3.rs-36867/v1 ◽

2020 ◽

Author(s):

Zhijun Zhao ◽

Jiquan Li ◽

Li Ma ◽

Hongmei Xue ◽

Xuxin Yang ◽

...

Keyword(s):

Tandem Repeats ◽

Brucella Melitensis ◽

Eastern Mediterranean ◽

Draft Genome ◽

Variable Number Tandem Repeat ◽

Variable Number ◽

Whole Genome ◽

Qinghai Province ◽

Evolutionary Origins ◽

Multiple Loci

Abstract Background Brucellosis, which is cause by Brucella, is one of the most important zoonoses and is considered a “forgotten, neglected zoonosis” by the WHO. Methods Blood samples were isolated from two brucellosis males that were confirmed B. melitensis positive following multiple loci variable-number tandem repeat analysis (MLVA) and strains QH2019001 and QH2019005 were identified. Genomic DNA was extracted from these samples and whole genome sequencing (WGS) was performed. Next, SNP-based phylogenetic analysis was performed to compare the two strains to 94 B. melitensis strains (complete genome and draft genome) retrieved from online databases. Results The QH2019001 and QH2019005 strains were found to have differences in their variable-number tandem repeats. Phylogenetic examination of the 96 strains assigned them to 5 genotype groups, with QH2019001 and QH2019005 assigned to the same group, but to different subgroups; with the QH2019005 strain assigned to a new subgenotype, IIj. These findings were then combined to determine strain origin. Conclusions Utilizing a whole genome SNP-based approach highlights the diversity between B. melitensis strains, and it can facilitate the elucidation of different evolutionary histories. This approach also revealed that the QH2019005 is part of a new subgenotype with an ancient origin in the eastern Mediterranean Sea.

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Variable Number Tandem Repeats mediate the expression of proximal genes

10.1101/2020.05.25.114082 ◽

2020 ◽

Cited By ~ 2

Author(s):

Mehrdad Bakhtiari ◽

Jonghun Park ◽

Yuan-Chun Ding ◽

Sharona Shleizer-Burko ◽

Susan L. Neuhausen ◽

...

Keyword(s):

Gene Expression ◽

Tandem Repeats ◽

Variable Number ◽

Maximum Effect ◽

Whole Genome ◽

Whole Genome Analysis ◽

Complex Disorders ◽

Genome Data ◽

Expression Of Genes ◽

Variable Number Tandem Repeats

AbstractVariable Number Tandem Repeats (VNTRs) account for a significant amount of human genetic variation. VNTRs have been implicated in both Mendelian and Complex disorders, but are largely ignored by whole genome analysis pipelines due to the complexity of genotyping and the computational expense. We describe adVNTR-NN, a method that uses shallow neural networks for fast read recruitment. On 55X whole genome data, adVNTR-NN genotyped each VNTR in less than 18 cpu-seconds, while maintaining 100% accuracy on 76% of VNTRs.We used adVNTR-NN to genotype 10,264 VNTRs in 652 individuals from the GTEx project and associated VNTR length with gene expression in 46 tissues. We identified 163 ‘eVNTR’ loci that were significantly associated with gene expression. Of the 22 eVNTRs in blood where independent data was available, 21 (95%) were replicated in terms of significance and direction of association. 49% of the eVNTR loci showed a strong and likely causal impact on the expression of genes and 80% had maximum effect size at least 0.3. The impacted genes have important role in complex phenotypes including Alzheimer’s, obesity and familial cancers. Our results point to the importance of studying VNTRs for understanding the genetic basis of complex diseases.

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MLVA-16 Genotyping of Brucella abortus and Brucella melitensis Isolates from Different Animal Species in Egypt: Geographical Relatedness and the Mediterranean Lineage

Pathogens ◽

10.3390/pathogens9060498 ◽

2020 ◽

Vol 9 (6) ◽

pp. 498

Author(s):

Gamal Wareth ◽

Mohamed El-Diasty ◽

Falk Melzer ◽

Gernot Schmoock ◽

Shawky A. Moustafa ◽

...

Keyword(s):

Genetic Diversity ◽

Animal Species ◽

Tandem Repeats ◽

Brucella Melitensis ◽

Variable Number ◽

Low Genetic Diversity ◽

Mediterranean Countries ◽

The Mediterranean ◽

Variable Number Tandem Repeats ◽

Open Markets

Brucellosis is a common zoonotic disease in Egypt. However, there are limited data available on the genetic diversity of brucellae circulating in Egypt and other Mediterranean areas. One hundred and nine Brucella (B.) strains were isolated from different animal species in thirteen Egyptian governorates. Multi-locus variable number tandem repeats (VNTRs) analysis (MLVA-16) was employed to determine the geographical relatedness and the genetic diversity of a panel of selected Egyptian strains (n = 69), with strains originating from Italy (n = 49), Portugal (n = 52), Greece (n = 63), and Tunisia (n = 4). Egyptian B. melitensis strains clustered into two main clusters containing 21 genotypes. Egyptian B. abortus strains clustered into three main clusters containing nine genotypes. The genotypes were irregularly distributed over time and space in the study area. Egyptian strains of B. melitensis showed MLVA-16 patterns closer to that of Italian strains. Egyptian B. abortus strains isolated from cattle share the same genotype with strains from Portugal and similar to strains from Italy with low genetic diversity. Strains with similar MLVA patterns isolated from different governorates highlight the movement of the pathogen among governorates. Hence, it may also reflect the long endemicity of brucellosis in Egypt with earlier dispersal of types and great local genetic diversity. Open markets may contribute to cross-species transmission and dissemination of the new types nationwide. The presence of West Mediterranean lineages of B. melitensis and relatedness of B. abortus strains from the studied countries is a result of the socio-historical connections among the Mediterranean countries. Transnational eradication of brucellosis in the Mediterranean basin is highly demanded.

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Molecular epidemiology of Brucella melitensis strains causing outbreaks in Croatia and Bosnia and Herzegovina

Acta Veterinaria Hungarica ◽

10.1556/004.2018.017 ◽

2018 ◽

Vol 66 (2) ◽

pp. 177-188 ◽

Cited By ~ 1

Author(s):

Sanja Duvnjak ◽

Ivana Račić ◽

Silvio Špičić ◽

Maja Zdelar-Tuk ◽

Irena Reil ◽

...

Keyword(s):

Bosnia And Herzegovina ◽

Tandem Repeats ◽

Brucella Melitensis ◽

Housekeeping Genes ◽

Variable Number ◽

Disease Spread ◽

Southeast Europe ◽

The Stability ◽

Variable Number Tandem Repeats ◽

Sequence Types

The most recent data on the incidence of brucellosis in Southeast Europe prove the persistence of this zoonosis in the area, regardless of constant efforts at controlling it as one of the most dangerous zoonoses. Forty-three Brucella melitensis strains were collected from cattle, sheep, goats and humans from Croatia as well as Bosnia and Herzegovina between 2009 and 2015. The strains were identified and genotyped in order to determine their epidemiological background. Standard biotyping methods and Bruce-ladder were used to identify the strains. Genotyping was done using multilocus variable number tandem repeats analysis (MLVA) on 16 and multilocus sequence typing analysis (MLST) on nine loci. Results were compared to each other and to internationally available data. Twenty- five novel genotypes and two sequence types were identified. All tested strains, apart from vaccine and reference strains, showed very close phylogenetic and geographic relationships. The genotyping results indicate the endemicity of brucellosis in this region. MLST showed no variation, confirming the stability of housekeeping genes. The results confirm already established routes of disease spread in this area, showing that a more detailed and vigorous control of this zoonosis is necessary.

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Investigation of the molecular characteristics of Brucella isolates from Guangxi Province, China

BMC Microbiology ◽

10.1186/s12866-019-1665-6 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 4

Author(s):

Zhi-guo Liu ◽

Miao Wang ◽

Hong-yan Zhao ◽

Dong-ri Piao ◽

Hai Jiang ◽

...

Keyword(s):

Brucella Melitensis ◽

Variable Number Tandem Repeat ◽

Genomic Analysis ◽

Public Health Problem ◽

Variable Number ◽

Comparative Genomic ◽

Human Brucellosis ◽

Molecular Characteristics ◽

Genetic Lineage ◽

Guangxi Province

Abstract Background Human brucellosis has become a severe public health problem in China’s Guangxi Province, and there has been higher prevalence of brucellosis in this region after 2010. Both multiple locus variable-number tandem repeat analysis (MLVA) and multilocus sequence typing (MLST) assay schedules were used to genotype isolates and determine relationships among isolates. Results A total of 40 isolates of Brucella were obtained from humans, pigs, and dogs from 1961 to 2016. There were at least three species of Brucella detected in Guangxi Province, Brucella melitensis, Brucella suis, and Brucella canis, with 16, 17, and 7 isolates, respectively. Of which B. suis biovar 3 was the predominant species resulting in pig brucellosis in the area examined before 2000s. Moreover, B. melitensis biovar 3 was found to be mainly responsible for human brucellosis during 2012–2016. All B. melitensis isolates in this study belonged to East Mediterranean lineage. MLVA-11 genotype 116 was the dominant genotype and represented 81.2% of the isolates. MLVA cluster analysis showed there to be 44% (7/16) brucellosis cases caused by B. melitensis with a profile of outbreak epidemic from 2012 to 2016. However, nearly 83.3% (20/24) of brucellosis cases resulting from both B. suis and B. canis showed no epidemiological links or sporadic characteristics. MLVA-16 analysis confirmed extensive genotype-sharing events between B. melitensis isolates from Guangxi and other northern provinces within China. These data revealed that there are potential epidemiology links among these strains. B. suis strains of this study showed a unique genetic lineage at the global level and may have existed historically in this area. However, present B. canis isolates were closely related to previously reported isolates in Korea, where they may have originated. MLST typing showed that the population structure of Brucella strains had changed considerably in this province; ST17 and ST21, two previously predominant populations appeared to have been replaced by recently emerging ST8 group. Conclusions Our investigation data have inspired the hypothesis that Guangxi Province had been subject to an imported human brucellosis epidemic. Our data suggest that strains found in Northern regions of China are the principal source of infections in recent cases of human brucellosis in Guangxi Province. Comparative genomic analysis from more strains is necessary to confirm this hypothesis. This work will facilitate better understanding of the epidemiology and improve the effectiveness of control and prevention of brucellosis in this region.

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Targeted Genotyping of Variable Number Tandem Repeats with adVNTR

10.1101/221754 ◽

2017 ◽

Cited By ~ 5

Author(s):

Mehrdad Bakhtiari ◽

Sharona Shleizer-Burko ◽

Melissa Gymrek ◽

Vikas Bansal ◽

Vineet Bafna

Keyword(s):

Single Molecule ◽

Sequence Variation ◽

Tandem Repeats ◽

Markov Models ◽

Repeat Unit ◽

Variable Number ◽

Repeat Sequence ◽

Whole Genome ◽

Single Nucleotide Variants ◽

Variable Number Tandem Repeats

AbstractWhole Genome Sequencing is increasingly used to identify Mendelian variants in clinical pipelines. These pipelines focus on single nucleotide variants (SNVs) and also structural variants, while ignoring more complex repeat sequence variants. We consider the problem of genotyping Variable Number Tandem Repeats (VNTRs), composed of inexact tandem duplications of short (6-100bp) repeating units. VNTRs span 3% of the human genome, are frequently present in coding regions, and have been implicated in multiple Mendelian disorders. While existing tools recognize VNTR carrying sequence, genotyping VNTRs (determining repeat unit count and sequence variation) from whole genome sequenced reads remains challenging. We describe a method, adVNTR, that uses Hidden Markov Models to model each VNTR, count repeat units, and detect sequence variation. adVNTR models can be developed for short-read (Illumina) and single molecule (PacBio) whole genome and exome sequencing, and show good results on multiple simulated and real data sets. adVNTR is available at https://github.com/mehrdadbakhtiari/adVNTR

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Slipped-Strand Mispairing at Noncontiguous Repeats in Poecilia reticulata: A Model for Minisatellite Birth

Genetics ◽

10.1093/genetics/155.3.1313 ◽

2000 ◽

Vol 155 (3) ◽

pp. 1313-1320 ◽

Cited By ~ 2

Author(s):

John S Taylor ◽

Felix Breden

Keyword(s):

Tandem Repeat ◽

Poecilia Reticulata ◽

Tandem Repeats ◽

Phylogenetic Reconstruction ◽

Variable Number ◽

Repeat Motif ◽

Raw Material ◽

Direct Repeats ◽

Mt Dna ◽

Variable Number Tandem Repeats

Abstract The standard slipped-strand mispairing (SSM) model for the formation of variable number tandem repeats (VNTRs) proposes that a few tandem repeats, produced by chance mutations, provide the “raw material” for VNTR expansion. However, this model is unlikely to explain the formation of VNTRs with long motifs (e.g., minisatellites), because the likelihood of a tandem repeat forming by chance decreases rapidly as the length of the repeat motif increases. Phylogenetic reconstruction of the birth of a mitochondrial (mt) DNA minisatellite in guppies suggests that VNTRs with long motifs can form as a consequence of SSM at noncontiguous repeats. VNTRs formed in this manner have motifs longer than the noncontiguous repeat originally formed by chance and are flanked by one unit of the original, noncontiguous repeat. SSM at noncontiguous repeats can therefore explain the birth of VNTRs with long motifs and the “imperfect” or “short direct” repeats frequently observed adjacent to both mtDNA and nuclear VNTRs.

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