A high degree of diversity was observed with 23 different STs identified. Virulence genes were determined by downloading core sequences from the virulence factor database (VFDB) and the National Center for Biotechnology Information (NCBI). Sequence types (STs) were determined in silico from the WGS data and isolates were assigned into clonal complexes (CCs) using the Campylobacter database. Campylobacter cgMLST and hierarchical clustering was performed by applying the single linkage algorithm. FastQ files were submitted to BioNumerics for analysis using the wgMLST scheme for allele calling.
GENETIC DISTANCES GENEIOUS PRIME SKIN
The aim was to exploit whole genome sequencing (WGS) to assess genomic diversity, identify virulence genes and deduce the proportion of Campylobacter colonized broilers that directly contaminate their carcasses.Ĭampylobacter jejuni isolates (107) from caeca and carcass neck skin samples (50 pairs from the same batch plus 7 individual caeca) sampled at three poultry slaughterhouses over a one-year period were selected for sequencing (MiSeq Illumina). However, resistance gene databases need curation and updates to revoke inaccuracy when using WGS-based analysis pipelines for AMR detection. Whole-genome sequencing can predict antimicrobial resistance with a high degree of accuracy. This study emphasized the potential of whole-genome sequencing to ameliorate the routine surveillance of C. Six isolates harbored a pTet-like plasmid-borne contig which carries the tet(O) gene. Out of 66 sequenced isolates, 28 (42.4%) carried plasmid-borne contigs. An assortment of 13 β-lactam resistance genes (blaOXA variants) was detected in 58 C. Five phenotypically erythromycin-susceptible isolates carried the mutation A103V in the gene for the ribosomal protein L22 inferring macrolide resistance. The single point mutation T86I in the housekeeping gene gyrA conferring resistance to quinolones was retrieved in 93.6% of phenotypically fluoroquinolone-resistant isolates. A gene cluster comprising the genes sat4, aph(3′)-IIIa and aadE was present in six isolates. The genes for resistance to ampicillin (blaOXA), tetracycline, neomycin, streptomycin (aadE) and streptothricin (sat4) were detected in isolated C. The wlaN gene associated with the Guillain–Barré syndrome was detected in nine (13.6%) isolates. Most of the isolates harbored the genes flaA (83.3%) and flaB (78.8%). Thirteen virulence-associated genes were identified in C. The average pairwise single nucleotide-polymorphisms distance of 14,585 SNPs (range: 0–26,540 SNPs) revealed a high genetic distinction between the isolates. The isolates were assigned to 28 different sequence types and 11 clonal complexes. Genetic resistance markers were identified with bioinformatics tools (AMRFinder, ResFinder, NCBI and ABRicate) and compared with the phenotypic antimicrobial resistance. Phylogeny, resistome, plasmidome and virulome profiles were analyzed using whole-genome sequencing data. Phenotypic antimicrobial resistance was determined. jejuni isolates obtained between 20 from commercial meat turkey flocks located in ten German federal states.
The Illumina MiSeq® technology was used to sequence 66 C. jejuni recovered from commercial turkey farms in Germany using whole-genome sequencing. The present investigation was designed to assess the epidemiology and genetic heterogeneity of C. Campylobacter (C.) jejuni is a zoonotic bacterium of public health significance.
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