Whole genome sequencing & bioinformatics of Campylobacter isolated from animals

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Date
2020-11
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G.B. Pant University of Agriculture and Technology, Pantnagar - 263145 (Uttarakhand)
Abstract
Campylobacter species are one of the leading cause of bacterial foodborne zoonoses. Worldwide, Pathogenic Campylobacter species are responsible for causing over 400–500 million infections cases each year. These pathogenic Campylobacter species are grouped into major human enteric pathogens (C. jejuni, C. jejuni subsp. jejuni (Cjj), C. jejuni subsp. doyley (Cjd), C. coli and C. fetus) minor pathogens (C. concisus, C. upsaliensis, C. lari and C. hyointestinalis) and major veterinary pathogens (C. fetus subsp. venerealis (Cfv) and C. Fetus subsp. fetus (Cff)). A total of 498 samples consisting of poultry caeca (120), litter (40), poultry rectal swabs (24), poultry skin (24), water samples (38),faeces of pigs (30), meat swabs (32), clinical dog faecal ssample (20), goat (32) and lab animals faeces (92) were screened for the presence of C. jejuni and C. coli using conventional isolation and identification procedures. The overall occurence of Campylobacter was 8.83 %. The samples collected were screened for campylobacters. Highest isolation rate was observed from lab animals (19.56 %, 18/92) followed by poultry caeca (13.33%,16/120), pig faeces (10%,3/30), meat swabs (9.37 %, 3/32) ,poultry faeces (7.14%, 3/42) and litter (2.5%, 1/40). Since loads of virulence genes are responsible for bacterial pathogenecity, resilence, stress response and environmental persistence. The individual detection of every gene by techniques like PCR is a tedious process. The next generation sequencing concept play an extremely important role in this context. Among next generation sequencing also, whole genome sequencing (WGS) and assembly is best method for the characterization of isolates as it can detect every gene of the organism coding for it’s identification, virulence, pathogenicity and antibiotic resistance.The study characterised the entire genome of the infectious isolates by analysis of WGS sequence data via use of both web based and command based tools. Virulence genes pattern was observed using web based analysis tools namely VFDB Virulence Factor Database (http://www.mgc.ac.cn/VFs) and wgMLST (Whole-genome MLST) which is pangenome based tool was used using core genome genes/loci and all acessory genes/loci to detect lineage – specific genes/loci. A total of 23 genes were detected by VFDB and 33 virulence genes were detected via SRST2. Only resistance to beta – lactam were found. Overall, our study detected only one antimicrobial resistance gene that is blaₒₓₐ -₄₈₉ commonly found in Campylobacter spp. indicating good antibiotic management in areas of Pantnagar, Rudrapur and Barielly
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