Journal Article

Genomic diversity of Campylobacter jejuni and Campylobacter coli isolated from the Ethiopian dairy supply chain

Pawar, Preeti, Johnson, Beth, Aurand-Cravens, Ashley, Dudley, Edward G., Admasie, Abera, Zewdu, Ashagrie, Kovac, Jasna, Sisay Tessema, Tesfaye, Burns, Logan, Voloshchuk, Olena, Wei, Xiaoyuan

2024

Overview

Campylobacteriosis outbreaks have previously been linked to dairy foods. While the genetic diversity of Campylobacter is well understood in high-income countries, it is largely unknown in low-income countries, such as Ethiopia. This study therefore aimed to conduct the first genomic characterization of Campylobacter isolates from the Ethiopian dairy supply chain to aid in future epidemiological studies. Fourteen C . jejuni and four C . coli isolates were whole genome sequenced using an Illumina platform. Sequences were analyzed using the bioinformatics tools in the GalaxyTrakr platform to identify MLST types, and single nucleotide polymorphisms, and infer phylogenetic relationships among the studied isolates. Assembled genomes were further screened to detect antimicrobial resistance and virulence gene sequences. Among 14 C . jejuni , ST 2084 and ST 51, which belong to the clonal complexes ST-353 and ST-443, respectively, were identified. Among the 4 sequenced C . coli isolates, two isolates belonged to ST 1628 and two to ST 830 from the clonal complex ST-828. The isolates of C . jejuni ST 2084 and ST 51 carried β-lactam resistance gene blaOXA-605 , a fluoroquinolone resistance-associated mutation T86I in the gryA gene, and a macrolide resistance-associated mutation A103V in 50S L22 . Only ST 2084 isolates carried the tetracycline resistance gene tetO . Conversely, all four C . coli ST 830 and ST 1628 isolates carried tetO , but only ST 1628 isolates also carried blaOXA-605 . Lastly, C . jejuni ST 2084 isolates carried a total of 89 virulence genes, and ST 51 isolates carried up to 88 virulence genes. Among C . coli , ST 830 isolates carried 71 genes involved in virulence, whereas two ST 1628 isolates carried up to 82 genes involved in virulence. Isolates from all identified STs have previously been isolated from human clinical cases, demonstrating a potential food safety concern. This finding warrants further monitoring of Campylobacter in dairy foods in Ethiopia to better understand and manage the risks associated with Campylobacter contamination and transmission.

• Publisher: Public Library of Science,Public Library of Science (PLoS)
• Subject: Agriculture / Amides / Analysis / Animals / Anti-Bacterial Agents - pharmacology / Antibiotics / Antimicrobial agents / Antimicrobial resistance / Beta lactamases / Biofilms / Bioinformatics / Biological diversity / Biology and Life Sciences / Campylobacter / Campylobacter coli - drug effects / Campylobacter coli - genetics / Campylobacter coli - isolation & purification / Campylobacter coli - pathogenicity / Campylobacter Infections - epidemiology / Campylobacter Infections - microbiology / Campylobacter jejuni - genetics / Campylobacter jejuni - isolation & purification / Campylobacter jejuni - pathogenicity / Campylobacteriosis / Dairy products / Dairy Products - microbiology / Drug resistance / Drug resistance in microorganisms / Drug Resistance, Bacterial - genetics / Epidemics / Epidemiology / Ethiopia - epidemiology / Food chains / Food contamination / Food contamination & poisoning / Food Microbiology / Food safety / Gene sequencing / Genes / Genetic aspects / Genetic diversity / Genetic Variation / Genome, Bacterial - genetics / Genomes / Genomics / Guillain-Barre syndrome / Humans / Logistics / Low income areas / Medicine and Health Sciences / Milk / Multilocus Sequence Typing / Mutation / Nucleotides / Pathogens / Phylogenetics / Phylogeny / Polymorphism, Single Nucleotide / Public health / Safety management / Single nucleotide polymorphisms / Single-nucleotide polymorphism / Supply chains / Taxonomy / Tetracycline / Tetracyclines / Value chain / Virulence / Virulence (Microbiology) / Virulence - genetics / Whole Genome Sequencing / β-Lactam antibiotics