Complete genome sequencing of four Arcobacter species reveals a diverse suite of mobile elements

Authors: Miller, William - Bill; Yee, Emma; Bono, James - Jim

Submitted to: Genome Biology and Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/17/2020
Publication Date: 2/3/2020
Citation: Miller, W.G., Yee, E., Bono, J.L. 2020. Complete genome sequencing of four Arcobacter species reveals a diverse suite of mobile elements. Genome Biology and Evolution. 12(2):3850–3856. https://doi.org/10.1093/gbe/evaa014.
DOI: https://doi.org/10.1093/gbe/evaa014

Interpretive Summary: Arcobacter species are routinely isolated from a large array of food animals (for example, chickens, cows and pigs), water, and shellfish (such as clams, mussels and oysters). Arcobacters have been implicated in human gastrointestinal illness and it is likely that the mode of transmission for these illnesses is via consumption of either contaminated food or water. DNA sequencing of the poultry isolate Arcobacter cibarius tentatively identified a large number of insertion sequences. Insertion sequences (IS) are mobile stretches of DNA that can insert copies of themselves into other regions of the chromosome, potentially disrupting gene function or transferring gene content within a bacterial strain or between strains. There are 29 families of insertion sequences currently described within bacteria. The chromosomes of A. cibarius and three other Arcobacters contained IS elements representing 13 of these families. Altogether, across 19 Arcobacter species, a total of 349 IS elements were identified, a number far higher than typical for related organisms, such as the pathogens Campylobacter jejuni and Helicobacter pylori. These elements are putatively associated with loss of motility, chromosomal rearrangements and antibiotic resistance gene transfer in Arcobacter, making them potentially an important component of Arcobacter biology.

Technical Abstract: Arcobacter species are recovered from a wide variety of sources, including animals, food, and both fresh and marine waters. Several Arcobacter species have also been recovered from human clinical samples and are thus associated tentatively with food- and water-borne human illnesses. Initial 454 sequencing of the poultry isolate Arcobacter cibarius H743 identified a large number and variety of potential insertion sequences. Large suites of mobile elements were also identified in the complete genomes of the A. acticola, A. pacificus and A. porcinus type strains. This study presents an analysis of the A. acticola, A. cibarius, A. pacificus and A. porcinus IS elements. The four genomes sequenced here contain 276 complete and degenerate IS elements, representing 13 of the current 29 prokaryotic IS element families. Expansion of the analysis to include 15 other Arcobacter spp. added 73 complete and degenerate IS elements. Several of these IS elements were identified in 2 or more Arcobacter species, suggesting movement by horizontal gene transfer between the arcobacters. These IS elements are putatively associated with intra-genomic deletions and inversions, and tentative movement of antimicrobial resistance genes. The A. cibarius strain H743 megaplasmid contains multiple IS elements common to the chromosome and, unusually, a complete ribosomal RNA locus, indicating that larger scale genomic rearrangements, potentially resulting from IS element-mediated megaplasmid cointegration and resolution may be occurring within A. cibarius and possibly other arcobacters. The presence of such a large and varied suite of mobile elements could have profound effects on Arcobacter biology and evolution.