AUTHOR=Zhao Hailan , Wang Jiaqi , Peng Yao , Cai Xunchao , Liu Yandi , Huang Wenqi , Huang Hongli , Nie Yuqiang 

TITLE=Genomic insights from Paraclostridium bifermentans HD0315_2: General features and pathogenic potential

JOURNAL=Frontiers in Microbiology

VOLUME=13

YEAR=2022

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2022.928153

DOI=10.3389/fmicb.2022.928153

ISSN=1664-302X

ABSTRACT=<sec><title>Background</title><p><italic>Paraclostridium bifermentans</italic> is the most diverse distributed species of <italic>Paraclostridium</italic> and can cause fatal human infections under rare conditions. However, its pathogenic mechanisms and adaptation ability behind infections remain unclear. Herein, we reported the complete genome sequence of <italic>P. bifermentans</italic> HD0315_2 isolated from the feces of a patient with Crohn's disease. Then, we performed genomic analyses to understand its pathogenic mechanisms and adaptation ability.</p></sec><sec><title>Results</title><p>The <italic>de novo</italic> assembly revealed that the HD0315_2 strain carried a circular chromosome of 3.27 Mb and six circular plasmids (19.41 to 139.50 kb). The phylogenomic analysis assigned the HD0315_2 strain as <italic>P. bifermentans</italic> and reclassified some previously non-<italic>P. bifermentans</italic> strains into this clade. The general genomic features showed that this species harbored a flexible genomic pool characterized by variable genome length and multiple plasmids. Then, the HD0315_2 strain was predicted as a human pathogen with high probability, and <italic>Listeria</italic> LIPI-1 virulence proteins were identified on its genome. Besides, abundant antibiotics/metal/stress resistant genes, such as <italic>asrABCH, cat, mccF, macB, entS, albA, bcrA</italic>, and <italic>tetB</italic>, were carried by either the genome or the plasmids. Furthermore, we proposed that transposase-directed horizontal gene transfer was responsible for the distribution of multiple copies of the <italic>hin</italic> gene in the plasmids.</p></sec><sec><title>Conclusion</title><p>The flexible genomic pool of <italic>P. bifermentans</italic> encodes abundant functions for antimicrobial or oxidative stress resistance, helping it successfully inhabit and adapt to diverse environments. Moreover, <italic>P. bifermentans</italic> HD0315_2 might infect hosts <italic>via</italic> a <italic>Listeria</italic> LIPI-1-like cycle, with the help of a plasmid expressing the Hin DNA invertase to evade host immune responses.</p></sec>