Introducing two new loci of VNTR9 and VNTR10 for Bordetella pertussis genotyping

Bordetella pertussis, the causative agent of whooping cough, continues to infect human hosts even in those populations where infants and children are routinely vaccinated. Causes of pertussis epidemiology are not fully identified unless strains of the pathogen are characterized by molecular means. Golbally, Multi Locus Variable Number of Tandem Repeats analysis (MLVA) has proved very useful in inter-laboratory surveillance of majoriy of world most important bacterial diseases. This work was conducted to improve the current MLVA typing method developed by Schouls in 2004.
An in silico search was comparatively conducted on the whole genomes of 5 laboratory/vaccine strains of B. pertussis deposited in the NCBI genome database by Tandem Repeat Finder software. PCR protocols were then adopted to enable simultaneous amplification found loci. A further comparative genomic analysis of 20 world-known B. pertussis strains from diverse spatial and temporal origins was performed using the detected new VNTR loci.
Two polymorphic loci carrying tandem repeats (TRs) with 6 (AAGCCC) and 9 (GGCTGGCCG) nucleotides were detected and designated as VNTR9 and VNTR10, respectively. Application of these on genomic templates from B. pertussis 107 and B. pertussis 509 vaccine strains used by Razi institute in manufacturing the pertussis vaccine resulted in succesful production of PCR amplicons from both strains. Nei's diversity indices of 0.38 and 0.1 were achieved by these loci, respectively in comparative genomic analysis of B. pertussis strains from across the world.
We assume inclusion of VNTR9 and VNTR10 in MLVA analysis of clinical isolates of B. pertussis is useful in improving current understanding of pertussis in Iran.