Genotyping of Bacillus anthracis strains based on automated capillary 25-loci Multiple Locus Variable-Number Tandem Repeats Analysis

Vector-borne generalist pathogens colonize several reservoir species and are usually dependent on polyphagous arthropods for dispersal; however, their spatial genetic structure is generally poorly understood. Using fast-evolving genetic markers (20 simple sequence repeat loci, resulting in a total of 119 alleles), we studied the genetic structure of the vector-borne plant-pathogenic bacterium Xylella fastidiosa in Napa Valley, CA, where it causes Pierce's disease when it is transmitted to grapevines from reservoir plants in adjacent

Section: Discussionmentioning

confidence: 99%

Spatial Genetic Structure of a Vector-Borne Generalist Pathogen

Coletta-Filho

Bittleston

Almeida

2011

“…Studies of genetic diversity of B. anthracis have relied on multiple-locus variable-number tandem repeat analysis (MLVA) (10,14,17), single-nucleotide polymorphisms (SNP) (15,17) and single-nucleotide repeat analysis (SNRA) (12,13,16). Keim et al described a hierarchical approach called PHRANA (progressive hierarchical resolving assays using nucleic acids) that uses markers that are progressively less stable but have increasing resolving power for typing B. anthracis (SNP, MLVA, and SNRA) (11).…”

mentioning

confidence: 99%

Genetic Diversity among Bacillus anthracis Soil Isolates at Fine Geographic Scales

Stratilo

Bader

2012

ABSTRACTEnvironmental samples were collected from carcass sites during and after anthrax outbreaks in 2000 and 2001 in the bison (Bison bison) population within Wood Buffalo National Park and the Hook Lake Region north of Wood Buffalo National Park.Bacillus anthracisspores were isolated from these samples and confirmed using phenotypic characterization and real-time PCR. ConfirmedB. anthracisisolates were typed using multiple-locus variable-number tandem repeat analysis (MLVA15) and single-nucleotide-repeat analysis (SNRA).B. anthracisisolates split into two clades based on MLVA15, while SNRA allowed some isolates between carcass sites to be distinguished from each other. SNRA polymorphisms were also present within a single carcass site. Some isolates from different carcass sites having the same SNRA type had divergent MLVA types; this finding leads to questions about hierarchical typing methods and the robustness of the fine-scale typing ofBacillus anthracis.

“…This could be due to the nature of the gel matrix, the slightly biased flanking sequences, or differences in mobility patterns of specific repeat units. The fragment size estimated by CE always shifts by a constant value (26,27). However, this did not interfere with the overall results, as the number of repeats interpreted by sequencing or CE generated the same MLVA type in each isolate.…”

Section: Bacterial Isolatesmentioning

confidence: 96%

Development of Multiple-Locus Variable-Number Tandem-Repeat Analysis for Molecular Subtyping of Campylobacter jejuni by Using Capillary Electrophoresis

Techaruvichit

Takahashi

Vesaratchavest³

et al. 2015

cCampylobacter jejuni is a common cause of the frequently reported food-borne diseases in developed and developing nations. This study describes the development of multiple-locus variable-number tandem-repeat (VNTR) analysis (MLVA) using capillary electrophoresis as a novel typing method for microbial source tracking and epidemiological investigation of C. jejuni. Among 36 tandem repeat loci detected by the Tandem Repeat Finder program, 7 VNTR loci were selected and used for characterizing 60 isolates recovered from chicken meat samples from retail shops, samples from chicken meat processing factory, and stool samples. The discrimination ability of MLVA was compared with that of multilocus sequence typing (MLST). MLVA (diversity index of 0.97 with 31 MLVA types) provided slightly higher discrimination than MLST (diversity index of 0.95 with 25 MLST types). The overall concordance between MLVA and MLST was estimated at 63% by adjusted Rand coefficient. MLVA predicted MLST type better than MLST predicted MLVA type, as reflected by Wallace coefficient (Wallace coefficient for MLVA to MLST versus MLST to MLVA, 86% versus 51%). MLVA is a useful tool and can be used for effective monitoring of C. jejuni and investigation of epidemics caused by C. jejuni. Campylobacter infection is one of the most commonly identified bacterial causes of acute gastroenteritis in humans worldwide (1). C. jejuni is the predominant species in the genus Campylobacter and is associated with human food-borne diseases. Usual symptoms of the infection caused by C. jejuni are fever, diarrhea, and abdominal cramps. Although infection with Campylobacter usually is not fatal, the reported cases of campylobacteriosis often exceed those of infections caused by the Salmonella species or Escherichia coli (2). In Japan, Campylobacter is one of the three main causes of food-borne diseases, with the estimated number of cases being around 1.5 million persons per year (3). Poultry products often are contaminated with C. jejuni, and most of the infections are found to be associated with the handling of raw poultry or eating raw or undercooked poultry meat (4, 5).Strain subtyping by molecular methods provides a powerful tool for epidemiological investigation and tracking the source of contamination (30, 31). To date, typing of C. jejuni strains was performed by random amplified polymorphic DNA analysis (8), amplified fragment length polymorphism (9), pulsed-field gel electrophoresis (10), ribotyping (9), flaA short variable region typing (11), microarray comparative genomic hybridization (12), repetitive sequence-based PCR fingerprinting (13), multilocus sequence typing (MLST) (14, 15), and whole-genome sequencing (WGS) (16). One of the most commonly used methods for C. jejuni typing in current research is MLST, which is considered the gold standard for the subtyping of C. jejuni. MLST of C. jejuni utilizes the sequence data obtained from seven housekeeping genes. The alleles from these housekeeping genes are assigned allele numbers based on a complete match ...