AUTHOR=Deblais Loic , Jang Hyein , Kauffman Mike , Gangiredla Jayanthi , Sawyer Marianne , Basa Saritha , Poelstra Jelmer W. , Babu Uma S. , Harrison Lisa M. , Hiett Kelli L. , Balan Kannan V. , Rajashekara Gireesh 

TITLE=Whole genome characterization of thermophilic Campylobacter species isolated from dairy manure in small specialty crop farms of Northeast Ohio

JOURNAL=Frontiers in Microbiology

VOLUME=14

YEAR=2023

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1074548

DOI=10.3389/fmicb.2023.1074548

ISSN=1664-302X

ABSTRACT=<sec><title>Introduction</title><p>With more public interest in consuming locally grown produce, small specialty crop farms (SSCF) are a viable and growing segment of the food production chain in the United States.</p></sec><sec><title>Methods</title><p>The goal of this study was to investigate the genomic diversity of <italic>Campylobacter</italic> isolated from dairy manure (<italic>n</italic> = 69) collected from 10 SSCF in Northeast Ohio between 2018 and 2020.</p></sec><sec><title>Results</title><p>A total of 56 <italic>C. jejuni</italic> and 13 <italic>C. coli</italic> isolates were sequenced. Multi-locus sequence typing (MLST) identified 22 sequence types (STs), with ST-922 (18%) and ST-61 (13%) predominant in <italic>C. jejuni</italic> and ST-829 (62%) and ST-1068 (38%) predominant in <italic>C. coli</italic>. Interestingly, isolates with similar genomic and gene contents were detected within and between SSCF over time, suggesting that <italic>Campylobacter</italic> could be transmitted between farms and may persist in a given SSCF over time. Virulence-associated genes (<italic>n</italic> = 35) involved in the uptake and utilization of potassium and organic compounds (succinate, gluconate, oxoglutarate, and malate) were detected only in the <italic>C. jejuni</italic> isolates, while 45 genes associated with increased resistance to environmental stresses (capsule production, cell envelope integrity, and iron uptake) were detected only in the <italic>C. coli</italic> isolates. <italic>Campylobacter coli</italic> isolates were also sub-divided into two distinct clusters based on the presence of unique prophages (<italic>n</italic> = 21) or IncQ conjugative plasmid/type-IV secretion system genes (<italic>n</italic> = 15). <italic>Campylobacter coli</italic> isolates harbored genes associated with resistance to streptomycin (<italic>aadE-Cc</italic>; 54%) and quinolone (<italic>gyrA-T86I</italic>; 77%), while <italic>C. jejuni</italic> had resistance genes for kanamycin (<italic>aph3’-IIIa</italic>; 20%). Both species harbored resistance genes associated with β-lactam (especially, <italic>blaOXA-193</italic>; up to 100%) and tetracycline (<italic>tetO</italic>; up to 59%).</p></sec><sec><title>Discussion/Conclusion</title><p>Our study demonstrated that <italic>Campylobacter</italic> genome plasticity associated with conjugative transfer might provide resistance to certain antimicrobials and viral infections <italic>via</italic> the acquisition of protein-encoding genes involved in mechanisms such as ribosomal protection and capsule modification.</p></sec>