scholarly journals Examination of Taxonomic Uncertainties Surrounding Brucella abortus bv. 7 by Phenotypic and Molecular Approaches

2013 ◽  
Vol 80 (5) ◽  
pp. 1570-1579 ◽  
Author(s):  
Bruno Garin-Bastuji ◽  
Virginie Mick ◽  
Gilles Le Carrou ◽  
Sebastien Allix ◽  
Lorraine L. Perrett ◽  
...  
Keyword(s):  
Brucella Abortus ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Epidemiological Methods ◽  
Content Type ◽  
Phenotypic Profile ◽  
Molecular Approaches ◽  
Content Classification ◽  
Species Specific ◽  
Kenyan Strain

ABSTRACTBrucellataxonomy is perpetually being reshuffled, at both the species and intraspecies levels. Biovar 7 ofBrucella abortuswas suspended from theApproved Lists of Bacterial NamesBrucellaclassification in 1988, because of unpublished evidence that the reference strain 63/75 was a mixture ofB. abortusbiovars 3 and 5. To formally clarify the situation, all isolates previously identified asB. abortusbv. 7 in the AHVLA and ANSES strain collections were characterized by classical microbiological and multiple molecular approaches. Among the 14 investigated strains, including strain 63/75, only four strains, isolated in Kenya, Turkey, and Mongolia, were pure and showed a phenotypic profile in agreement with the former biovar 7, particularly agglutination with both anti-A/anti-M monospecific sera. These results were strengthened by molecular strategies. Indeed, genus- and species-specific methods allowed confirmation that the four pure strains belonged to theB. abortusspecies. The combination of most approaches excluded their affiliation with the recognized biovars (biovars 1 to 6 and 9), while some suggested that they were close to biovar 3.These assays were complemented by phylogenetic and/or epidemiological methods, such as multilocus sequence analysis (MLSA) and variable-number tandem repeat (VNTR) analysis. The results of this polyphasic investigation allow us to propose the reintroduction of biovar 7 into theBrucellaclassification, with at least three representative strains. Interestingly, the Kenyan strain, sharing the same biovar 7 phenotype, was genetically divergent from other three isolates. These discrepancies illustrate the complexity ofBrucellataxonomy. This study suggests that worldwide collections could include strains misidentified asB. abortusbv. 7, and it highlights the need to verify their real taxonomic position.

scholarly journals Isolation and Molecular Characterization ofBrucellaIsolates in Cattle Milk in Uganda

2015 ◽  
Vol 2015 ◽  
pp. 1-9 ◽  
Author(s):  
Denis Rwabiita Mugizi ◽  
Shaman Muradrasoli ◽  
Sofia Boqvist ◽  
Joseph Erume ◽  
George William Nasinyama ◽  
...  
Keyword(s):  
Risk Factors ◽  
Genetic Variation ◽  
Brucella Abortus ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Infected Cattle ◽  
Milk Samples ◽  
Molecular Approaches ◽  
Epidemiological Tool ◽  
The World

Brucellosis is endemic in livestock and humans in Uganda and its transmission involves a multitude of risk factors like consumption of milk from infected cattle. To shed new light on the epidemiology of brucellosis in Uganda the present study used phenotypic and molecular approaches to delineate theBrucellaspecies, biovars, and genotypes shed in cattle milk.Brucella abortuswithout a biovar designation was isolated from eleven out of 207 milk samples from cattle in Uganda. These isolates had a genomic monomorphism at 16 variable number tandem repeat (VNTR) loci and showed in turn high levels of genetic variation when compared with other African strains or otherB. abortusbiovars from other parts of the world. This study further highlights the usefulness of MLVA as an epidemiological tool for investigation ofBrucellainfections.

scholarly journals Link between Geographical Origin and Occurrence of Brucella abortus Biovars in Cow and Water Buffalo Herds

2012 ◽  
Vol 79 (3) ◽  
pp. 1039-1043 ◽  
Author(s):  
Giorgia Borriello ◽  
Simone Peletto ◽  
Maria G. Lucibelli ◽  
Pier L. Acutis ◽  
Danilo Ercolini ◽  
...  
Keyword(s):  
Brucella Abortus ◽  
Water Buffalo ◽  
Geographical Origin ◽  
Variable Number Tandem Repeat ◽  
Geographic Origin ◽  
Variable Number ◽  
National Plan ◽  
Content Type ◽  
Repeat Analysis ◽  
Management Procedures

ABSTRACTSixty-threeBrucellaisolates from water buffaloes and cattle slaughtered within the Italian national plan for brucellosis control were characterized by multiple-locus variable-number tandem repeat analysis (MLVA). Genotyping indicated a strong influence of geographic origin on theBrucella abortusbiovar distribution in areas where brucellosis is endemic and highlighted the importance of rigorous management procedures aimed at avoiding inter- and intraherd spreading of pathogens.

scholarly journals Molecular Epidemiology of Brucella abortus Isolates from Cattle, Elk, and Bison in the United States, 1998 to 2011

2012 ◽  
Vol 78 (10) ◽  
pp. 3674-3684 ◽  
Author(s):  
James Higgins ◽  
Tod Stuber ◽  
Christine Quance ◽  
William H. Edwards ◽  
Rebekah V. Tiller ◽  
...  
Keyword(s):  
Brucella Abortus ◽  
Minimum Spanning Tree ◽  
Variable Number Tandem Repeat ◽  
The United States ◽  
Variable Number ◽  
Group Method ◽  
Content Type ◽  
Field Isolates ◽  
Pair Group ◽  
Starr County

ABSTRACTA variable-number tandem repeat (VNTR) protocol targeting 10 loci in theBrucella abortusgenome was used to assess genetic diversity among 366 field isolates recovered from cattle, bison, and elk in the Greater Yellowstone Area (GYA) and Texas during 1998 to 2011. Minimum spanning tree (MST) and unweighted-pair group method with arithmetic mean (UPGMA) analyses of VNTR data identified 237 different VNTR types, among which 14 prominent clusters of isolates could be identified. Cattle isolates from Texas segregated into three clusters: one comprised of field isolates from 1998 to 2005, one comprised of vaccination-associated infections, and one associated with an outbreak in Starr County in January 2011. An isolate obtained from a feral sow trapped on property adjacent to the Starr County herd in May 2011 clustered with the cattle isolates, suggesting a role for feral swine asB. abortusreservoirs in Starr County. Isolates from a 2005 cattle outbreak in Wyoming displayed VNTR-10 profiles matching those of strains recovered from Wyoming and Idaho elk. Additionally, isolates associated with cattle outbreaks in Idaho in 2002, Montana in 2008 and 2011, and Wyoming in 2010 primarily clustered with isolates recovered from GYA elk. This study indicates that elk play a predominant role in the transmission ofB. abortusto cattle located in the GYA.

scholarly journals Host Range-Associated Clustering Based on Multilocus Variable-Number Tandem-Repeat Analysis, Phylotypes, and Virulence Genes of Atypical EnteropathogenicEscherichia coliStrains

2019 ◽  
Vol 85 (6) ◽  
Author(s):  
Md Shafiullah Parvej ◽  
Hiromi Nakamura ◽  
Md Ashraful Alam ◽  
Lili Wang ◽  
Shaobo Zhang ◽  
...  
Keyword(s):  
Spanning Tree ◽  
Virulence Genes ◽  
Minimum Spanning Tree ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Epidemiological Methods ◽  
Content Type ◽  
Repeat Analysis ◽  
Group I ◽  
Virulence Group

ABSTRACTAtypical enteropathogenicEscherichia coli(aEPEC) strains (36 Japanese and 50 Bangladeshi) obtained from 649 poultry fecal samples were analyzed by molecular epidemiological methods. Clermont’s phylogenetic typing showed that group A was more prevalent (58%, 50/86) than B1 (31%, 27/86). Intimin type β1, which is prevalent among human diarrheal patients, was predominant in both phylogroups B1 (81%, 22/27) and A (70%, 35/50). However, about 95% of B1-β1 strains belonged to virulence group I, and 77% of them were Japanese strains, while 17% (6/35) of A-β1 strains did. Multilocus variable-number tandem-repeat analysis (MLVA) distributed the strains into 52 distinct profiles, with Simpson’s index of diversity (D) at 73%. When the data were combined with those of 142 previous strains from different sources, the minimum spanning tree formed five zones for porcine strains, poultry strains (excluding B1-β1), strains from healthy humans, bovine and human patient strains, and the B1-β1 poultry strains. Antimicrobial resistance to nalidixic acid was most common (74%) among the isolates. Sixty-eight percent of them demonstrated resistance to ≥3 antimicrobial agents, and most of them (91%) were from Bangladesh. The strains were assigned into two groups by hierarchical clustering. Correlation matrix analysis revealed that the virulence genes were negatively associated with antimicrobial resistance. The present study suggested that poultry, particularly Japanese poultry, could be another reservoir of aEPEC (phylogroup B1, virulence group I, and intimin type β1); however, poultry strains seem to be apart from patient strains that were closer to bovine strains. Bangladeshi aEPEC may be less virulent for humans but more resistant to antibiotics.IMPORTANCEAtypical enteropathogenicEscherichia coli(aEPEC) is a diarrheagenic type ofE. coli, as it possesses the intimin gene (eae) for attachment and effacement on epithelium. Since aEPEC is ubiquitous even in developed countries, we previously used molecular epidemiological methods to discriminate aEPEC as a human pathogen. The present study assessed poultry as another source of human diarrheagenic aEPEC. Poultry could be the source of aEPEC (phylogroup B1, virulence group I, and intimin type β1) found among patient strains in Japan. However, the minimum spanning tree (MST) suggested that the strains from Japanese poultry were far from Japanese patient strains compared with the distance between bovine and patient strains. Bangladeshi avian strains seemed to be less diarrheagenic but are hazardous as a source of drug resistance genes.

scholarly journals Potentially Human-Pathogenic Escherichia coli O26 in Norwegian Sheep Flocks

2011 ◽  
Vol 77 (14) ◽  
pp. 4949-4958 ◽  
Author(s):  
C. Sekse ◽  
M. Sunde ◽  
B.-A. Lindstedt ◽  
P. Hopp ◽  
T. Bruheim ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Human Pathogens ◽  
Content Type ◽  
Representative Sampling ◽  
E Coli ◽  
Pathogenic Escherichia Coli ◽  
Close Relationship ◽  
Large Survey

ABSTRACTA national survey ofEscherichia coliO26 in Norwegian sheep flocks was conducted, using fecal samples to determine the prevalence. In total, 491 flocks were tested, andE. coliO26 was detected in 17.9% of the flocks. One hundred forty-twoE. coliO26 isolates were examined for flagellar antigens (H typing) and four virulence genes, includingstxandeae, to identify possible Shiga toxin-producingE. coli(STEC) and enteropathogenicE. coli(EPEC). Most isolates (129 out of 142) were identified asE. coliO26:H11. They possessedeaeand may have potential as human pathogens, although only a small fraction were identified as STEC O26:H11, giving a prevalence in sheep flocks of only 0.8%. Correspondingly, the sheep flock prevalence of atypical EPEC (aEPEC) O26:H11 was surprisingly high (15.9%). The genetic relationship between theE. coliO26:H11 isolates was investigated by pulsed-field gel electrophoresis (PFGE) and multilocus variable number tandem repeat analysis (MLVA), identifying 63 distinct PFGE profiles and 22 MLVA profiles. Although the MLVA protocol was less discriminatory than PFGE and a few cases of disagreement were observed, comparison by partition mapping showed an overall good accordance between the two methods. A close relationship between a few isolates of aEPEC O26:H11 and STEC O26:H11 was identified, but all theE. coliO26:H11 isolates should be considered potentially pathogenic to humans. The present study consisted of a representative sampling of sheep flocks from all parts of Norway. This is the first large survey of sheep flocks focusing onE. coliO26 in general, including results of STEC, aEPEC, and nonpathogenic isolates.

scholarly journals Prediction of Local Transmission of Mycobacterium tuberculosis Isolates of a Predominantly Beijing Lineage by Use of a Variable-Number Tandem-Repeat Typing Method Incorporating a Consensus Set of Hypervariable Loci

2017 ◽  
Vol 56 (1) ◽  
Author(s):  
Yoshiro Murase ◽  
Kiyohiko Izumi ◽  
Akihiro Ohkado ◽  
Akio Aono ◽  
Kinuyo Chikamatsu ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Tandem Repeat ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Trend Test ◽  
Typing Method ◽  
Content Type ◽  
Tuberculosis Transmission ◽  
High Prevalence ◽  
Hypervariable Loci

ABSTRACT Strain genotyping based on the variable-number tandem repeat (VNTR) is widely applied for identifying the transmission of Mycobacterium tuberculosis. A consensus set of four hypervariable loci (1982, 3232, 3820, and 4120) has been proposed to improve the discrimination of Beijing lineage strains. Herein, we evaluated the utility of these four hypervariable loci for tracing local tuberculosis transmission in 981 cases over a 14-month period in Japan (2010 to 2011). We used six different VNTR systems, with or without the four hypervariable loci. Patient ages and weighted standard distances (a measure of the dispersion of genotype-clustered cases) were used as proxies for estimating local tuberculosis transmission. The highest levels of isolate discrimination were achieved with VNTR systems that incorporated the four hypervariable loci (i.e., the Japan Anti-Tuberculosis Association [JATA]18-VNTR, mycobacterial interspersed repetitive unit [MIRU]28-VNTR, and 24Beijing-VNTR). The clustering rates by JATA12-VNTR, MIRU15-VNTR, JATA15-VNTR, JATA18-VNTR, MIRU28-VNTR, and 24Beijing-VNTR systems were 52.2%, 51.0%, 39.0%, 24.1%, 23.1%, and 22.0%, respectively. As the discriminative power increased, the median weighted standard distances of the clusters tended to decrease (from 311 to 80 km, P < 0.001, Jonckheere-Terpstra trend test). Concurrently, the median ages of patients in the clusters tended to decrease (from 68 to 60 years, P < 0.001, Jonckheere-Terpstra trend test). These findings suggest that strain typing using the four hypervariable loci improves the prediction of active local tuberculosis transmission. The four-locus set can therefore contribute to the targeted control of tuberculosis in settings with high prevalence of Beijing lineage strains.

scholarly journals Approaches to gene mapping in complex disorders and their application in child psychiatry and psychology

2001 ◽  
Vol 179 (2) ◽  
pp. 122-128 ◽  
Author(s):  
Philip J. Asherson ◽  
Sarah Curran
Keyword(s):  
Reading Disability ◽  
Molecular Genetics ◽  
Molecular Mechanisms ◽  
Variable Number Tandem Repeat ◽  
Twin Studies ◽  
Variable Number ◽  
Chromosome 15 ◽  
Complex Disorders ◽  
Molecular Approaches ◽  
Genes And Environment

BackgroundTwin studies demonstrate the importance of genes and environment in the aetiology of childhood psychiatric and neurodevelopmental disorders. Advances in molecular genetics enable the identification of genes involved in complex disorders and enable the study of molecular mechanisms and gene–environment interactions.AimsTo review the role of molecular genetics studies in childhood behavioural and developmental traits.MethodMolecular approaches to complex disorders are reviewed, with examples from autism, reading disability and attention-deficit hyperactivity disorder (ADHD).ResultsThe most robust finding in ADHD is the association of a variable number tandem repeat polymorphism in exon 3 of the DRD4 gene. Other replicated associations with ADHD are outlined in the text. In autism, there is a replicated linkage finding on chromosome 7. Linkage studies in reading disability have confirmed a locus on chromosome 6 and strongly suggest one on chromosome 15.ConclusionsIn the next 5–10 years susceptibility genes for these disorders will be established. Describing their relationship to biological and behavioural function will be a far greater challenge.

scholarly journals Antimicrobial Resistance and Virulence Determinants in European Salmonella Genomic Island 1-Positive Salmonella enterica Isolates from Different Origins

2011 ◽  
Vol 77 (16) ◽  
pp. 5655-5664 ◽  
Author(s):  
Janine Beutlich ◽  
Silke Jahn ◽  
Burkhard Malorny ◽  
Elisabeth Hauser ◽  
Stephan Hühn ◽  
...  
Keyword(s):  
Multidrug Resistance ◽  
Antimicrobial Resistance ◽  
Salmonella Enterica ◽  
Genomic Island ◽  
Variable Number Tandem Repeat ◽  
Tetracycline Resistance ◽  
Variable Number ◽  
Virulence Determinants ◽  
Content Type ◽  
Strain Collection

ABSTRACTSalmonellagenomic island 1 (SGI1) contains a multidrug resistance region conferring the ampicillin-chloramphenicol-streptomycin-sulfamethoxazole-tetracycline resistance phenotype encoded byblaPSE-1,floR,aadA2,sul1, andtet(G). Its increasing spread via interbacterial transfer and the emergence of new variants are important public health concerns. We investigated the molecular properties of SGI1-carryingSalmonella entericaserovars selected from a European strain collection. A total of 38 strains belonging toS. entericaserovar Agona,S. entericaserovar Albany,S. entericaserovar Derby,S. entericaserovar Kentucky,S. entericaserovar Newport,S. entericaserovar Paratyphi B dT+, andS. entericaserovar Typhimurium, isolated between 2002 and 2006 in eight European countries from humans, animals, and food, were subjected to antimicrobial susceptibility testing, molecular typing methods (XbaI pulsed-field gel electrophoresis [PFGE], plasmid analysis, and multilocus variable-number tandem-repeat analysis [MLVA]), as well as detection of resistance and virulence determinants (PCR/sequencing and DNA microarray analysis). Typing experiments revealed wide heterogeneity inside the strain collection and even within serovars. PFGE analysis distinguished a total of 26 different patterns. In contrast, the characterization of the phenotypic and genotypic antimicrobial resistance revealed serovar-specific features. Apart from the classical SGI1 organization found in 61% of the strains, seven different variants were identified with antimicrobial resistance properties associated with SGI1-A (S. Derby), SGI1-C (S. Derby), SGI1-F (S. Albany), SGI1-L (S. Newport), SGI1-K (S. Kentucky), SGI1-M (S.Typhimurium), and, eventually, a novel variant similar to SGI1-C with additional gentamicin resistance encoded byaadB. Only minor serovar-specific differences among virulence patterns were detected. In conclusion, the SGI1 carriers exhibited pathogenetic backgrounds comparable to the ones published for susceptible isolates. However, because of their multidrug resistance, they may be more relevant in clinical settings.

scholarly journals Phylogenetic and Variable-Number Tandem-Repeat Analyses Identify Nonpathogenic Xanthomonas arboricola Lineages Lacking the Canonical Type III Secretion System

2015 ◽  
Vol 81 (16) ◽  
pp. 5395-5410 ◽  
Author(s):  
Salwa Essakhi ◽  
Sophie Cesbron ◽  
Marion Fischer-Le Saux ◽  
Sophie Bonneau ◽  
Marie-Agnès Jacques ◽  
...  
Keyword(s):  
Tandem Repeat ◽  
Type Iii Secretion ◽  
Variable Number Tandem Repeat ◽  
Type Iii Secretion System ◽  
Variable Number ◽  
Secretion System ◽  
Content Type ◽  
Type Iii ◽  
Xanthomonas Arboricola ◽  
Canonical Type

ABSTRACTXanthomonas arboricolais conventionally known as a taxon of plant-pathogenic bacteria that includes seven pathovars. This study showed thatX. arboricolaalso encompasses nonpathogenic bacteria that cause no apparent disease symptoms on their hosts. The aim of this study was to assess theX. arboricolapopulation structure associated with walnut, including nonpathogenic strains, in order to gain a better understanding of the role of nonpathogenic xanthomonads in walnut microbiota. A multilocus sequence analysis (MLSA) was performed on a collection of 100X. arboricolastrains, including 27 nonpathogenic strains isolated from walnut. Nonpathogenic strains grouped outside clusters defined by pathovars and formed separate genetic lineages. A multilocus variable-number tandem-repeat analysis (MLVA) conducted on a collection ofX. arboricolastrains isolated from walnut showed that nonpathogenic strains clustered separately from clonal complexes containingXanthomonas arboricolapv. juglandis strains. Some nonpathogenic strains ofX. arboricoladid not contain the canonical type III secretion system (T3SS) and harbored only one to three type III effector (T3E) genes. In the nonpathogenic strains CFBP 7640 and CFBP 7653, neither T3SS genes nor any of the analyzed T3E genes were detected. This finding raises a question about the origin of nonpathogenic strains and the evolution of plant pathogenicity inX. arboricola. T3E genes that were not detected in any nonpathogenic isolates studied represent excellent candidates to be those responsible for pathogenicity inX. arboricola.

scholarly journals Molecular Epidemiology Characteristics of Brucella Abortus Strains in China and Their Relationships With World Lineages

2020 ◽  
Author(s):  
Xu-Ming Wang ◽  
Zhongzhi Zhao ◽  
Miao Wang ◽  
Buyun Cui ◽  
Zhiguo Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Epidemiology ◽  
Brucella Abortus ◽  
Variable Number Tandem Repeat ◽  
Northern China ◽  
Variable Number ◽  
Snp Analysis ◽  
High Genetic Diversity ◽  
Geographic Origins ◽  
Epidemic Area

Abstract Background Brucella abortus is a facultative intracellular Gram-negative bacterium that causes chronic persistent infections in humans and livestock. In this study, conventional bio-typing, multiple-locus variable-number tandem repeat analysis (MLVA), and whole-genome sequencing-single-nucleotide polymorphism (WGS-SNP) were used to investigate the molecular epidemiology characteristics of Brucella abortus strains in China and their relationships to world lineages. Results A total of 100 strains were collected from 1953 to 2013, suggesting that B. abortus circulated in China in the past five decades. Moreover, most strains were mainly distributed in the Northwest areas, suggest that provinces in the Northwest were a dominant epidemic area of this disease. During this period, seven biovars were found, indicating that B. abortus had a high diversity of biovars and it is also a potential reason for the disease ongoing spread in the Northern provinces. Strains have high genetic diversity, and bruce07 is the most helpful locus for genotyping of this population. Moreover, 17 MLVA-11 genotypes were found; 13 of them are of known genotypes and four are unassigned genotypes, indicating that B. abortus in this study had several geographic origins. Still, strains from unassigned genotypes may originate from China. Many shared MLVA-16 genotypes were observed in strains from the same provinces in Northern China, which confirmed a B. abortus brucellosis outbreak within Northern regions. WGS-SNP analysis showed that eight Chinese strains formed a ladder-like phylogram (C. Ⅶ) with strains from nine countries, including Uganda, Iraq, Russia, Georgia, Spain, Italy, Egypt, Mongolia, and China; suggest that strains were introduced to these countries from a single source. Conclusions Chinese B. abortus strains had high biovars and genetic diversity as well as represent characteristics of multiple geographic origins, and B. abortus strains from several mainly epidemic areas were closely related to strains from Russia and Mongolia; frequent animal (cattle) trade and exchanges may promote this process. We will provide new and valuable information to strengthening surveillance and control of B. abortus brucellosis in China.

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