IN-SILICO AND EXPERIMENTAL ANALYSES OF INTEGRATIVE AND CONJUGATIVE ELEMENTS OF THE SXT/R391 TYPE 1 FAMILY REVEAL A HIGHLY VARIABLE GENE CONTENT AND A SPECIES-SPECIFIC DISSEMINATION

DANIELA PIRAJAN; ANDRES IRIARTE; SUSANA VAZQUEZ; CECILIA QUIROGA

Chapadmalal

Congreso; XVIII SAMIGE; 2023

SAMIGE

The Integrative and Conjugative Elements (ICEs) of the SXT/R391 family participate in the transfer of genetic material between bacteria contributing to the spread of genetic traits to different habitats. Their structure consists of several conserved core regions (xis/int, traID, traLEKBVA, traCFWUN, bet/exo, traFHG, and setCDR), interrupted by genes encoding metal or antimicrobial resistance genes (ARGs), mobile genetic elements (MGEs), distinct defense systems (DSs), as well as other beneficial genes. The aim of this work was to evaluate the occurrence of this ICE family in bacteria isolated from different reservoirs and to identify the beneficial genes encoded in these platforms. We performed an in-silico search for these elements in 68120 complete genomes available in Genbank as of May 7, 2022. We detected 147 ICEs SXT/R391 distributed among Enterobacterales (66), Vibrionales (52), Alteromonadales (26), Pasteurellales (1), Thiotrichales (1), and Oceanospirillales (1). Bacteria harboring these SXT/R391 ICEs were widely distributed in different habitats, -clinical (39), aquatic (34), animal-host (51), human-impacted niches (10), and roots (1). The analysis of the SXT/R391 platform showed that all were inserted in the prfC gene, corresponding to the canonical type 1 structure. Their genetic content was analyzed using ISFinder v2.0, CARD v4.0, PADLOC v1.1.0, DefenseFinder v1.0.2, and TADB 2.0 programs, which revealed the presence of 236 MGEs, 57 ARGs, 69 systems related to operons associated with metal reduction, transport, or efflux and 440 DSs. In addition, we looked for these ICE in clinical (64) and Antarctic (53) isolates by PCR targeting conserved genes (setC, setD, traV, bet, and exo). We found 6 SXT/R391 ICEs in multidrug resistant Proteus mirabilis (2) and Providencia stuartii (4) isolates recovered from a public hospital of Buenos Aires city. P. stuartii CQ32 genome was sequenced using the MiSeq Illumina Technology, assembled using SPAdes v.3.13.0 and analyzed with the previous tools, which allowed us to confirm the presence of a type 1 SXT/R391 ICE inserted at prfC harboring all core genes and the abortive infection systems Lamassu and AbiE, as well as a type I BREX phage exclusion system. Our work suggests that there is a bias of the SXT/R391 ICEs towards Proteus, Providencia, and Vibrio genera and members from Alteromonadales order. These ICEs regularly carry a variety of accessory genes (ARG, MGE or DS), which contribute to the host survival in different niches. Furthermore, the marked co-occurrence of defense systems within the SXT/R391 ICEs suggests that these platforms collaborate with the host protection against foreign MGEs.