Genetic diversity and epidemiology of accessory gene regulator loci in Clostridioides difficile

Abstract

Quorum sensing is known to regulate bacterial virulence, and the accessory gene regulator (agr) loci is one of the genetic loci responsible for its regulation. Recent reports examining Clostridioides difficile show that two agr loci, agr1 and agr2, regulate toxin production, but the diversity of agr loci and their epidemiology is unknown. In our study, in silico analysis was performed to research genetic diversity of agr, and C. difficile isolates from clinical samples underwent multilocus sequence typing (MLST) and PCR analysis of agr loci. To reveal the distribution of agr among different strains, phylogenetic analysis was also performed. In our in silico analysis, two different subtypes, named agr2R and agr2M, were found in agr2, which were previously reported. PCR analysis of 133 C . difficile isolates showed that 131 strains had agr1, 61 strains had agr2R, and 26 strains had agr2M; agr2R was mainly found in clade 1 or clade 2 organisms, whereas agr2M was only found in clade 4. With rare exception, agr1-negative sequence types (STs) belonged to clade C-Ⅰ and C-Ⅲ, and one clade 4 strain had agr2R. Our study revealed subtypes of agr2 not previously recognized, and the distribution of several agr loci in C. difficile . These findings provide a foundation for further functional and clinical research of the agr loci.

Assessment of the Transmission Dynamics of Clostridioides difficile in a Farm Environment Reveals the Presence of a New Toxigenic Strain Connected to Swine Production

“…To our knowledge, this is the first report of an agr1like locus in an MGE. Considering the role agr genes pose in contributing to the virulence and colonization factors by quorum sensing regulation (Darkoh et al, 2017), the presence of such element in a prophage that can be subjected to horizontal gene transfer, may influence the behavior of the bacterial community considered in this study (Hargreaves et al, 2014;Okada et al, 2020). Further studies are still needed to uncover the role of this third agr1-like locus in the PT RT033 clone, but it is possible that it may influence biofilm production through quorum sensing regulation contributing to bacterial persistence in the environment, thus allowing for the maintenance of the transmission cycle.…”

Update on Commonly Used Molecular Typing Methods for Clostridioides difficile

“…This type of gene has been implicated in the regulation of several characteristics related to C. difficile virulence, including flagellar biosynthesis, production of the toxin TcdA, and signaling proteins involved in cyclic dimeric GMP (c-di-GMP) signaling [ 145 ]. Notably, the distribution of agr gene variants differs among clades, with agr2R -positive strains primarily found in Clades 1 and 2, and STs carrying agr2M exclusively identified within Clade 4 [ 146 ]. It has also been hypothesized that host response, rather than ST or strain characteristics, plays a major role in the development of the disease [ 147 ].…”

The RgaS-RgaR two-component system promotes Clostridioides difficile sporulation through a small RNA and the Agr1 system

“…The majority of C . difficile genomes encode an agrB1D1 operon with no apparent cognate agrA1 or agrC1 present [ 29 , 31 – 33 ]. Recent work revealed that the agrB1D1 locus positively impacts early sporulation gene expression and spore formation [ 34 ]; however, the identity of the AgrD1 receptor remains elusive.…”

“…Prior studies in Clostridium botulinum, Clostridium sporogenes, and Clostridium perfringens demonstrated that disruption or knockdown of the agrBD genes resulted in decreased spore formation [29,30]. The majority of C. difficile genomes encode an agrB1D1 operon with no apparent cognate agrA1 or agrC1 present PLOS GENETICS [29,[31][32][33]. Recent work revealed that the agrB1D1 locus positively impacts early sporulation gene expression and spore formation [34]; however, the identity of the AgrD1 receptor remains elusive.…”