Despite shared geography, Campylobacter isolated from surface water are genetically distinct from Campylobacter isolated from chickens

Authors: Meinersmann, Richard - Rick; Berrang, Mark; SHARIAT, NIKKI - University Of Georgia; RICHARDS, AMBER - University Of Georgia; Miller, William - Bill

Submitted to: Microbiology Spectrum
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/31/2023
Publication Date: 3/2/2023
Citation: Meinersmann, R.J., Berrang, M.E., Shariat, N.W., Richards, A.K., Miller, W.G. 2023. Despite shared geography, Campylobacter isolated from surface water are genetically distinct from Campylobacter isolated from chickens. Microbiology Spectrum. 11(2). Article e04147-22. https://doi.org/10.1128/spectrum.04147-22.
DOI: https://doi.org/10.1128/spectrum.04147-22

Interpretive Summary: n general, bacteria in the same habitat will share genetic material, especially if they are the same species. This can be seen as many genes having identical sequences despite evolutionary distance between the observed individuals. This is a product of the transfer of chunks of DNA, including whole genes, between the individuals. Such exchanges are known to occur among Campylobacter jejuni, a human pathogen that commonly is found in chickens without harm to the chicken. We hypothesized that Campylobacter from chickens would be found in nearby environmental waterways. However, in the Northeastern community of Georgia that we surveyed, there was virtually no evidence of exchange of DNA between chicken and river isolates of Campylobacter. We surmised from this that there were possibly physiological barriers to the exchange of DNA between these populations of the bacteria. Two known physiological barrier mechanisms in bacteria that very specifically recognize DNA from different populations are clustered regularly interspaced palindromic repeats (CRISPRs) and restriction/modification enzyme systems. We surveyed our populations of chicken and river Campylobacter for specific forms of these two systems. We found that the two populations had different specificities of their barrier systems. At this time, we cannot determine if the differences are the cause or the result of the segregation of the populations of Campylobacter. Further research may show the root cause of the segregation of these populations that can be developed into a barrier of the species from chickens.

Technical Abstract: The relationship of Campylobacter jejuni found in chickens to those found in environmental waters, either as a reservoir, a source, or downstream deposition, is an open question. We tested the hypothesis that Campylobacter isolated from chicken ceca and river water in an overlapping geographic area would share genetic information. In the years 2012 and 2013, we collected 67 isolates of C. jejuni from chicken ceca at a commercial slaughter plant in northeast Georgia, USA, and 39 isolates of C. jejuni from rivers and creeks in the same watershed. Isolates were subjected to whole genome sequencing and the data used for core genome multi-locus sequence typing (cgMLST). Cluster analysis showed that there were four distinct subpopulations; 56 chicken isolates were in one main subpopulation and 32 water isolates were in another. Seven chicken isolates and eleven water isolates formed two distinct outgroups that were less distant from each other than the main subpopulations were. Calculation of fixation statistic (Fst) showed that all four subpopulations were significantly distinct. Analyses of Fst on a locus-by-locus basis of pairings of the main subpopulation showed that greater than 90% of the loci were differentiated by subpopulation. In the smaller subpopulations from chicken and water, approximately 63% of the loci were differentiated according to source. Only 2 genes showed clear differentiation of both chicken subpopulations from both water subpopulations. Phage sequence fragments of the CJIE4 family were found frequently in the main chicken subpopulation and the water outgroup subpopulation but were found sparsely in the main water population and not at all in the chicken outgroup. CRISPR spacers that targeted the phage sequences were common in the main water subpopulation, only once in the main chicken subpopulation and not at all in the chicken or water outgroups. Restriction enzyme genes also showed a biased distribution. These data suggest that there is little transfer of C. jejuni genetic material between chickens and nearby river water. Campylobacter differentiation according to these two sources does not show clear evidence of evolutionary selection; the differentiation is probably due to geospatial isolation, genetic drift and the action of CRISPRs and restriction enzymes.