Abstract
The genus Shewanella consists of facultatively anaerobic Gram-negative bacteria, which are regarded as potential agents of food contamination and opportunistic human pathogens. Information about the distribution and genetic characteristics of SXT/R391 integrative conjugative elements (ICEs) in Shewanella species is limited. Here, 91 Shewanella strains collected from diverse samples in China were studied for the presence of SXT/R391 ICEs. Three positive strains, classified as Shewanella upenei, were obtained from patients and water from a local mill. In light of their close clonal relationships and high sequence similarity, a representative ICE was selected and designated ICESupCHN110003. The BLASTn searches against GenBank showed that ICEVchBan5 was most closely related to ICESupCHN110003, with the coverage of 76% and identity of 99%. The phylogenetic tree of concatenated core genes demonstrated that ICESupCHN110003 formed a distinct branch outside the cluster comprising ICEValA056-1, ICEPmiCHN2410, and ICEPmiChn1. Comparison of the genetic structures revealed that ICESupCHN110003 encoded uncommon genes in hotspots, such as specific type III restriction-modification system, conferring adaptive functions to the host. Based on the low coverage in the sequence analysis, independent clade in the phylogenetic tree, and unique inserted fragments in hotspots, ICESupCHN110003 represented a novel SXT/R391 element, which widened the list of ICEs. Furthermore, the antibiotic resistance genes floR, strA, strB, and sul2 in ICESupCHN110003 and resistance to multiple drugs of the positive isolates were detected. A cross-species transfer capability of the SXT/R391 ICEs was also discovered. In summary, it is necessary to reinforce continuous surveillance of SXT/R391 ICEs in the genus Shewanella.
Highlights
In the last two decades, it has become known that horizontal gene transfer (HGT) plays a leading role in the evolutionary and environmental adaptation of bacteria (Hacker and Kaper, 2000; Juhas et al, 2009)
Another six Shewanella isolates were obtained from the brine and bean curd; these isolates were negative for SXT/R391 elements and were confirmed as strains of S. haliotis (Supplementary Figure S1)
SXT/R391 integrative conjugative elements (ICEs) have been investigated in the genera Vibrio (Wang et al, 2016), Providencia (Coetzee et al, 1972), Photobacterium (Nonaka et al, 2012), Proteus
Summary
In the last two decades, it has become known that horizontal gene transfer (HGT) plays a leading role in the evolutionary and environmental adaptation of bacteria (Hacker and Kaper, 2000; Juhas et al, 2009). ICEs comprise a large number of self-transmissible elements, which can integrate into bacterial chromosomes, excise from their host chromosome, form a transient circular intermediate, transfer to another cell and reintegrate into the new host’s chromosome at the target site (Burrus et al, 2006; Wozniak and Waldor, 2010). SXT/R391 ICEs have been found in different sources, including clinical, food, and environmental samples, and they share a conserved integrase that mediates the integration into the 5 end of the prfC gene in the host chromosome (Burrus et al, 2006; Wozniak et al, 2009). SXT and R391 have been grouped in an ICE family containing 52 nearly identical core genes. Some of them are involved in the process of integration/excision, conjugative transfer, and regulation, while other core genes may encode functions that enhance ICE fitness to the environment. In addition to the core modules, five hotspots (HS1–5) and four variable regions (VRI–VRIV) have been reported, which contain inserted variable genes conferring resistance to antibiotics and heavy metals (Wozniak et al, 2009; Lei et al, 2016)
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