Genome analysis of a clinical isolate of Shewanella sp. uncovered an active hybrid integrative and conjugative element carrying an integron platform inserted in a novel genomic locus

Abstract

Shewanella spp. are currently considered emerging pathogens that can code for a blaOXA carbapenemase in their chromosome. Complete genome analysis of the clinical isolate Shewanella sp. Sh95 revealed that this strain is a novel species that shares a lineage with marine isolates. Characterization of its resistome showed that it codes for genes drfA15, qacH and blaOXA-48. We propose that Shewanella sp. Sh95 acts as reservoir of blaOXA-48. Moreover, mobilome analysis showed that it contains a novel ICE, named ICESh95. Comparative analysis between the close relatives ICESpuPO1 from Shewanella sp. W3-18-1 and ICE SXTMO10 from Vibrio cholerae showed that ICESh95 encompassed two new regions, a type III restriction modification system and a multidrug resistance integron. The integron platform contained a novel arrangement formed by gene cassettes drfA15 and qacH and a class C-attC group II intron. Furthermore, insertion of ICESh95 occurred at a unique target site, which correlates with the presence of a different xis/int module. Mobility of ICESh95 was assessed showing its ability to self-transfer at high levels to different bacteria species. The presence of a highly adaptable element capable of acquiring antibiotic resistance determinants, combined with its efficient activity to self-transfer makes this element a clear threat for the control of the dissemination of antimicrobial resistance; a troublesome scenario when natural bacteria from water ecosystems, such as Shewanella, act as vector in its propagation.