Genomic analysis points to multiple genetic mechanisms for non-transformable Campylobacter jejuni ST-50

Authors: Parker, Craig; VILLAFUERTE, DAVID - North Carolina State University; Miller, William - Bill; Huynh, Steven; Chapman, Mary; HANAFY, ZAHRA - North Carolina State University; JACKSON III, JAMES - North Carolina State University; MILLER, MORGAN - North Carolina State University; KATHARIOU, SOPHIA - North Carolina State University

Submitted to: Microorganisms
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/30/2024
Publication Date: 2/4/2024
Citation: Parker, C.T., Villafuerte, D.A., Miller, W.G., Huynh, S., Chapman, M.H., Hanafy, Z., Jackson Iii, J.H., Miller, M.A., Kathariou, S. 2024. Genomic analysis points to multiple genetic mechanisms for non-transformable Campylobacter jejuni ST-50. Microorganisms. 12(2). Article 327. https://doi.org/10.3390/microorganisms12020327.
DOI: https://doi.org/10.3390/microorganisms12020327

Interpretive Summary: Campylobacter jejuni and C. coli are the most common causative agent of bacterial gastroenteritis worldwide. These campylobacters are gram-negative, obligately microaerophilic, spiral-shaped, and highly motile bacteria that frequently colonize poultry, cattle and swine. They are well known for their natural competence, i.e., their capacity to uptake naked DNA and subsequent transformation. This trait may play major roles in the notable genetic diversity of these species as well as their capacity to acquire antimicrobial resistance (AMR) determinants. Naturally occurring non-competent strains have been reported, but their prevalence among the Campylobacter population remains poorly understood. Analysis of 25 U.S. poultry-associated (US) C. jejuni and C. coli strains possessing few or no AMR determinants identified 13 that were non-transformable to nalidixic acid resistance, including both available C. jejuni strains of ST50. Examination of 36 additional C. jejuni ST50 strains from poultry, cattle, and swine in the U.S showed these additional strains were non-transformable. Genomic analysis of the ST50 strains identified presence of prophage nucleases associated with C. jejuni integrated elements (CJIE). Additionally, certain ST50 strains had loss-of-function mutations in cts genes that encode the competence, DNA uptake machinery. The presence of a DNase or the loss of the competence machinery likely reduced transformability of these strains. C. jejuni ST50 is found worldwide and analysis of the genomes of ST50 strains from Europe and North America show a high incidence of CJIE nucleases among ST50 strains. However, cts mutations were mainly associated with strains with U.S. origin. Most C. jejuni ST50 strains from the U.S. harbored few or no AMR determinants. The selective forces driving non-transformability of C. jejuni ST50 strains in the U.S. remain to be elucidated. The current findings suggest that the lack of competence of this major clone may lead to a less diverse clonal lineage with impaired capacity for AMR acquisition.

Technical Abstract: Campylobacter jejuni and Campylobacter coli are well known for their natural competence, i.e., their capacity for the uptake of naked DNA with subsequent transformation. This study identifies non-transformable C. jejuni and C. coli strains from domestic animals and employs genomic analysis to investigate the strain genotypes and their associated genetic mechanisms. The results reveal genetic associations leading to a non-transformable state, including functional DNase genes from bacteriophages and mutations within the cts-encoded DNA-uptake system, which impact the initial steps of the DNA uptake during natural transformation. Interestingly, all 38 tested C. jejuni ST-50 strains from the United States exhibit a high prevalence of non-transformability, and the strains harbor a variety of these genetic markers. This research emphasizes the role of these genetic markers in hindering the transfer of antimicrobial resistance (AMR) determinants, providing valuable insights into the genetic diversity of Campylobacter. As ST-50 is a major clone of C. jejuni globally, we additionally determined the prevalence of the genetic markers for non-transformability among C. jejuni ST-50 from different regions of the world, revealing distinct patterns of evolution and a strong selective pressure on the loss of competence in ST-50 strains, particularly in the agricultural environment in the United States. Our findings contribute to a comprehensive understanding of genetic exchange mechanisms within Campylobacter strains, and their implications for antimicrobial resistance dissemination and evolutionary pathways within specific lineages.