scholarly journals Genetic Traces of the Francisella tularensis Colonization of Spain, 1998–2020

2020 ◽  
Vol 8 (11) ◽  
pp. 1784
Author(s):  
Kerstin Myrtennäs ◽  
Raquel Escudero ◽  
Ángel Zaballos ◽  
Rosa González-Martín-Niño ◽  
Miklós Gyuranecz ◽  
...  
Keyword(s):  
Capillary Electrophoresis ◽  
Francisella Tularensis ◽  
Tandem Repeats ◽  
Geographical Area ◽  
Variable Number ◽  
Nucleotide Polymorphisms ◽  
Short Read ◽  
Snp Data ◽  
Genetic Clustering ◽  
Causative Bacterium

More than 1000 humans have acquired the febrile disease tularemia in Spain since the first notification of human cases in 1997. We here aimed to study the recent molecular evolution of the causative bacterium Francisella tularensis during disease establishment in Spain. Single-nucleotide polymorphisms (SNPs) and variable-number tandem repeats (VNTRs) were analyzed in whole-genome sequences (WGS) of F. tularensis. Short-read WGS data for 20 F. tularensis strains from humans infected in the periods 2014–2015 and 2018–2020 in Spain were generated. These data were combined with WGS data of 25 Spanish strains from 1998 to 2008 and two reference strains. Capillary electrophoresis data of VNTR genetic regions were generated and compared with the WGS data for the 11 strains from 2014 to 2015. Evolutionary relationships among strains were analyzed by phylogenetic methods. We identified 117 informative SNPs in a 1,577,289-nucleotide WGS alignment of 47 F. tularensis genomes. Forty-five strains from Spain formed a star-like SNP phylogeny with six branches emerging from a basal common node. The most recently evolved genomes formed four additional star-like structures that were derived from four branches of the basal common node. VNTR copy number variation was detected in two out of 10 VNTR regions examined. Genetic clustering of strains by VNTRs agreed with the clustering by SNPs. The SNP data provided higher resolution among strains than the VNTRs data in all but one cases. There was an excellent correlation between VNTR marker sizing by capillary electrophoresis and prediction from WGS data. The genetic data strongly support that tularemia, indeed, emerged recently in Spain. Distinct genetic patterns of local F. tularensis population expansions imply that the pathogen has colonized a previously disease-free geographical area. We also found that genome-wide SNPs provide higher genetic resolution among F. tularensis genomes than the use of VNTRs, and that VNTR copy numbers can be accurately predicted using short-read WGS data.

scholarly journals Can 15-Locus Mycobacterial Interspersed Repetitive Unit-Variable-Number Tandem Repeat Analysis Provide Insight into the Evolution of Mycobacterium tuberculosis?

2005 ◽  
Vol 71 (12) ◽  
pp. 8207-8213 ◽  
Author(s):  
Andrea Gibson ◽  
Timothy Brown ◽  
Lucy Baker ◽  
Francis Drobniewski
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Tandem Repeats ◽  
Variable Number Tandem Repeat ◽  
Epidemiological Studies ◽  
Variable Number ◽  
Molecular Techniques ◽  
Nucleotide Polymorphisms ◽  
East African ◽  
Phylogeny And Evolution ◽  
Phylogenetic Lineages

ABSTRACT The phylogeny and evolution of the bacterium Mycobacterium tuberculosis is still poorly understood despite the application of a variety of molecular techniques. We analyzed 469 M. tuberculosis and 49 Mycobacterium bovis isolates to evaluate if the mycobacterial interspersed repetitive units-variable-number tandem repeats (MIRU-VNTR) commonly used for epidemiological studies can define the phylogeny of the M. tuberculosis complex. This population was characterized by previously identified silent single-nucleotide polymorphisms (sSNPs) or by a macroarray based on these sSNPs that was developed in this study. MIRU-VNTR phylogenetic codes capable of differentiating between phylogenetic lineages were identified. Overall, there was 90.9% concordance between the lineages of isolates as defined by the MIRU-VNTR and sSNP analyses. The MIRU-VNTR phylogenetic code was unique to M. bovis and was not observed in any M. tuberculosis isolates. The codes were able to differentiate between different M. tuberculosis strain families such as Beijing, Delhi, and East African-Indian. Discrepant isolates with similar but not identical MIRU-VNTR codes often displayed a stepwise trend suggestive of bidirectional evolution. A lineage-specific panel of MIRU-VNTR can be used to subdivide each lineage for epidemiological purposes. MIRU-VNTR is a valuable tool for phylogenetic studies and could define an evolutionarily uncharacterized population of M. tuberculosis complex organisms.

Rapid multiple-locus variable-number tandem-repeats analysis of Shigella spp. using multicolour capillary electrophoresis

2010 ◽  
Vol 83 (3) ◽  
pp. 279-285 ◽  
Author(s):  
Monica Rawal ◽  
Elsebeth Hoff ◽  
Lena Aas-Pedersen ◽  
Kjersti Haugum ◽  
Bjørn-Arne Lindstedt
Keyword(s):  
Capillary Electrophoresis ◽  
Tandem Repeats ◽  
Variable Number ◽  
Multiple Locus ◽  
Shigella Spp ◽  
Variable Number Tandem Repeats

scholarly journals Characterization and genotyping of strains of Francisella tularensis isolated in Bulgaria

2009 ◽  
Vol 58 (1) ◽  
pp. 82-85 ◽  
Author(s):  
Krustyu T. Marinov ◽  
Elena D. Georgieva ◽  
Ivan N. Ivanov ◽  
Todor V. Kantardjiev
Keyword(s):  
Francisella Tularensis ◽  
Acid Production ◽  
Tandem Repeats ◽  
Variable Number ◽  
Variable Number Tandem Repeats

A tularaemia focus was detected in 1998 in Bulgaria, in an area where tularaemia had never been reported. The properties of Francisella tularensis subsp. holarctica strains isolated from 1998 to 2005 were studied. The strains showed heterogeneity, based on acid production from glycerol and erythromycin susceptibility. Genotyping by analysis of seven loci containing variable-number tandem repeats showed four genotypes among eight strains.

scholarly journals Pulmonary Tuberculosis Outbreak in a High School, China

2021 ◽  
Vol 5 (1) ◽  
Author(s):  
◽  
Yang Zhou ◽  
Bing Zhao ◽  
Tao Li ◽  
Qian Cheng ◽  
...  
Keyword(s):  
High School ◽  
Mycobacterium Tuberculosis ◽  
Tandem Repeats ◽  
Skin Testing ◽  
Drug Susceptibility ◽  
Variable Number ◽  
Hunan Province ◽  
Tuberculin Skin Testing ◽  
Nucleotide Polymorphisms ◽  
Symptom Screening

This study reports an outbreak of Tuberculosis (TB) in a high school in Hunan province, China during January 2017-April 2018. Contact investigation and TB screening were conducted through symptom screening, tuberculin skin testing, chest radiography and smear examination. Identification of positive isolates and drug susceptibility phenotype were assessed by standard method. Mycobacterial Interspersed Repetitive Units-Variable Number Tandem Repeats (MIRU-VNTR) and Whole Genome Sequencing (WGS) were performed to investigate the relationships among the positive isolates. A total of 90 students and one teacher were diagnosed active pulmonary TB among 2908 students and 188 staff, with an attack rate of 2.94%. Thirteen positive isolates were identified as drug susceptible Beijing family of Mycobacterium tuberculosis. Results of MIRU-VNTR typing and WGS revealed two clones of Mycobacterium tuberculosis circulating during outbreak. One hundred and twenty-nine Single Nucleotide Polymorphisms (SNPs) discriminated the isolates in two clusters; the maximum number of SNPs between any pair of isolates in each cluster was five or fewer. Our findings highlight the importance of early identification and isolation of the TB cases to prevent spread of TB. WGS provides better resolution than MIRU-VNTR to identify recent transmission in TB outbreak.

Association of the NOS3 intron-4 VNTR polymorphism with aneurysmal subarachnoid hemorrhage

2014 ◽  
Vol 121 (3) ◽  
pp. 587-592 ◽  
Author(s):  
Jonatan Myrup Staalsø ◽  
Troels Edsen ◽  
Alexandros Kotinis ◽  
Bertil Romner ◽  
Jacob Bertram Springborg ◽  
...  
Keyword(s):  
Nitric Oxide ◽  
Subarachnoid Hemorrhage ◽  
Tandem Repeats ◽  
Aneurysmal Subarachnoid Hemorrhage ◽  
Variable Number ◽  
Oxide System ◽  
Stepwise Logistic Regression ◽  
Nucleotide Polymorphisms ◽  
Common Genetic Variants ◽  
Intron 4

Object The nitric oxide system has been linked to the pathogenesis of aneurysmal subarachnoid hemorrhage (SAH). The authors performed a case-control study to investigate the association between SAH and common genetic variants within the endothelial nitric oxide synthase gene (NOS3). Methods Three hundred thirty-three Caucasian SAH patients and 498 controls were genotyped for the –922A > G (rs 1800779), –786T > C (rs2070744), and 894G > T (rs1799983) single nucleotide polymorphisms and the intron-4 27-bp variable number of tandem repeats polymorphism (27-bp-VNTR). Results The b/b (5 repeats) genotype of the 27-bp-VNTR was overrepresented in cases (77%) versus controls (69%) (p = 0.02). In male patients the b/b genotype was found in 85% compared with 67% in male controls, whereas in women, the frequencies were 73% and 72%, respectively. This corresponds to an odds ratio of 2.8 (95% CI 1.5–5.6, p = 0.0005) for SAH in men with the b/b genotype versus men with a/b or a/a. In women, no such association was found (OR 1.1, 95% CI 0.7–1.6, p = 0.76). Stepwise logistic regression including arterial hypertension, smoking, sex, and age with interactions yielded similar effect estimates of the 27-bp-VNTR. Haplotype analysis revealed that no single haplotype containing the b-allele was responsible for the observed genotype effect. Conclusions The authors' results suggest that the NOS3 27-bp-VNTR b/b genotype independent of other risk factors act in concert with male sex to substantially increase risk of SAH. This effect is not mediated by any single NOS3 haplotype.

Genetic diversity of theMycobacterium tuberculosisBeijing family based on multiple genotyping profiles

2015 ◽  
Vol 144 (8) ◽  
pp. 1728-1735 ◽  
Author(s):  
Y. LIU ◽  
S. WANG ◽  
H. LU ◽  
W. CHEN ◽  
W. WANG
Keyword(s):  
Genetic Diversity ◽  
Tandem Repeats ◽  
Cross Sectional Study ◽  
Variable Number ◽  
Beijing Genotype ◽  
Nucleotide Polymorphisms ◽  
Beijing Family ◽  
Cross Sectional ◽  
Discriminatory Ability ◽  
Family Based

SUMMARYAmong the most prevalentMycobacterium tuberculosis(Mtb) strains worldwide is the Beijing genotype, which has caused large outbreaks of tuberculosis (TB). Characteristics facilitating the dissemination of Beijing family strains remain unknown, but they are presumed to have been acquired through evolution of the lineage. To explore the genetic diversity of the Beijing family Mtb and explore the discriminatory ability of mycobacterial interspersed repetitive units-variable number of tandem repeats (MIRU-VNTR) loci in several regions of East Asia, a cross-sectional study was conducted with a total of 163 Beijing strains collected from registered TB patients between 1 June 2009 and 31 November 2010 in Funing County, China. The isolated strains were analysed by 15-MIRU-VNTR loci typing and compared with published MIRU-VNTR profiles of Beijing strains. Synonymous single nucleotide polymorphisms at 10 chromosomal positions were also analysed. The combination of SNP and MIRU-VNTR typing may be used to assess Mtb genotypes in areas dominated by Beijing strains. The modern subfamily in Shanghai overlapped with strains from other countries, whereas the ancient subfamily was genetically differentiated across several countries. Modern subfamilies, especially ST10, were prevalent. Qub11b and four other loci (MIRU 26, Mtub21, Qub26, Mtub04) could be used to discriminate Beijing strains.

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