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The SXT\/R391 family of ICEs was defined based on the conservation of a core set of 52 genes and site-specific integration into the 5\u2032 end of the chromosomal gene<jats:italic>prfC<\/jats:italic>. Hence, the integrase gene<jats:italic>int<\/jats:italic>has been intensively used as a marker to detect SXT\/R391 ICEs in clinical isolates. ICEs sharing most core genes but differing by their integration site and integrase gene have been recently reported and excluded from the SXT\/R391 family. Here we explored the prevalence and diversity of atypical ICEs in GenBank databases and their relationship with typical SXT\/R391 ICEs. We found atypical ICEs in<jats:named-content content-type=\"genus-species\">V. cholerae<\/jats:named-content>isolates that predate the emergence and expansion of typical SXT\/R391 ICEs in the mid-1980s in seventh-pandemic toxigenic<jats:named-content content-type=\"genus-species\">V. cholerae<\/jats:named-content>strains O1 and O139. Our analyses revealed that while atypical ICEs are not associated with antibiotic resistance genes, they often carry cation efflux pumps, suggesting heavy metal resistance. Atypical ICEs constitute a polyphyletic group likely because of occasional recombination events with typical ICEs. Furthermore, we show that the alternative integration and excision genes of atypical ICEs remain under the control of SetCD, the main activator of the conjugative functions of SXT\/R391 ICEs. Together, these observations indicate that substitution of the integration\/excision module and change of specificity of integration do not preclude atypical ICEs from inclusion into the SXT\/R391 family.<\/jats:p><jats:p><jats:bold>IMPORTANCE<\/jats:bold><jats:named-content content-type=\"genus-species\">Vibrio cholerae<\/jats:named-content>is the causative agent of cholera, an acute intestinal infection that remains to this day a world public health threat. Integrative and conjugative elements (ICEs) of the SXT\/R391 family have played a major role in spreading antimicrobial resistance in seventh-pandemic<jats:named-content content-type=\"genus-species\">V. cholerae<\/jats:named-content>but also in several species of<jats:named-content content-type=\"genus-species\">Enterobacteriaceae<\/jats:named-content>. Most epidemiological surveys use the integrase gene as a marker to screen for SXT\/R391 ICEs in clinical or environmental strains. With the recent reports of closely related elements that carry an alternative integrase gene, it became urgent to investigate whether ICEs that have been left out of the family are a liability for the accuracy of such screenings. In this study, based on comparative genomics, we broaden the SXT\/R391 family of ICEs to include atypical ICEs that are often associated with heavy metal resistance.<\/jats:p>","DOI":"10.1128\/aem.00485-18","type":"journal-article","created":{"date-parts":[[2018,4,16]],"date-time":"2018-04-16T08:42:15Z","timestamp":1523868135000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":42,"title":["Redefinition and Unification of the SXT\/R391 Family of Integrative and Conjugative Elements"],"prefix":"10.1128","volume":"84","author":[{"given":"Audrey","family":"Bioteau","sequence":"first","affiliation":[{"name":"D\u00e9partement de biologie, Universit\u00e9 de Sherbrooke, Sherbrooke, Quebec, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Romain","family":"Durand","sequence":"additional","affiliation":[{"name":"D\u00e9partement de biologie, Universit\u00e9 de Sherbrooke, Sherbrooke, Quebec, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6318-6904","authenticated-orcid":false,"given":"Vincent","family":"Burrus","sequence":"additional","affiliation":[{"name":"D\u00e9partement de biologie, Universit\u00e9 de Sherbrooke, Sherbrooke, Quebec, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_3_2_2","first-page":"225","article-title":"Antimicrobials & cholera: are we stranded","volume":"133","author":"Ghosh A","year":"2011","unstructured":"Ghosh A, Ramamurthy T. 2011. 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