Whole-genome sequencing reveals changes in genomic diversity and distinctive repertoires of T3SS and T6SS effector candidates in Chilean clinical Campylobacter strains

Abstract

Campylobacter is the leading cause of bacterial gastroenteritis worldwide and an emerging and neglected pathogen in South America. This zoonotic pathogen colonizes the gastrointestinal tract of a wide range of mammals and birds, with poultry as the most important reservoir for human infections. Apart from its high morbidity rates, the emergence of resistant strains is of global concern. The aims of this work were to determine genetic diversity, presence of antimicrobial resistance determinants and virulence potential of Campylobacter spp. isolated from patients with acute gastrointestinal disease at ‘Clinica Alemana’, Santiago de Chile. The study considered the isolation of Campylobacter spp., from stool samples during a 20-month period (January 2020 to September 2021). We sequenced (NextSeq, Illumina) and performed an in-depth analysis of the genome sequences of 88 Campylobacter jejuni and 2 Campylobacter coli strains isolated from clinical samples in Chile. We identified a high genetic diversity among C. jejuni strains and the emergence of prevalent clonal complexes, which were not identified in our previous reports. While ~40% of strains harbored a mutation in the gyrA gene associated with fluoroquinolone resistance, no macrolide-resistance determinants were detected. Interestingly, gene clusters encoding virulence factors such as the T6SS or genes associated with long-term sequelae such as Guillain-Barré syndrome showed lineage-relatedness. In addition, our analysis revealed a high degree of variability regarding the presence of fT3SS and T6SS effector proteins in comparison to type strains 81-176, F38011, and NCTC 11168 and 488. Our study provides important insights into the molecular epidemiology of this emerging foodborne pathogen. In addition, the differences observed regarding the repertoire of fT3SS and T6SS effector proteins could have an impact on the pathogenic potential and transmissibility of these Latin American isolates, posing another challenge in characterizing the infection dynamics of this emergent and neglected bacterial pathogen.

Prevalence and genetic characterization of Campylobacter from clinical poultry cases in China

“…Furthermore, the WGS data were used to identify antimicrobial resistance genes and virulence genes. Antimicrobial resistance determinants were screened in each Campylobacter genome using ABRicate, which includes the Resfinder, CARD, ARG-ANNOT, and NCBI ARRGD databases ( 25 ). Regarding macrolides, two markers of antimicrobial resistance, including the A2075G mutation in the gene encoding 23S rRNA and the ermB gene, were analyzed ( 26 ).…”

“…Regarding macrolides, two markers of antimicrobial resistance, including the A2075G mutation in the gene encoding 23S rRNA and the ermB gene, were analyzed ( 26 ). gyrA and 23S RNA gene point mutations were determined using Resfinder ( 25 ). The bla OXA605 -positive isolates were screened for the single-nucleotide mutation (transversion G→T) in the promoter region of the target gene.…”

Campylobacter jejuni virulence factors: update on emerging issues and trends

“…In addition to the T3SS, a T6SS has also been found in C. jejuni . Interestingly, only ~ 16–20% of C. jejuni isolates have been shown to encode the T6SS [ 53 , 54 ]. The C. jejuni T6SS has been shown to play a role in its adhesion and invasion of T84 colonic epithelial cells and murine macrophages, as well as in enabling colonisation in a murine model [ 53 ].…”