Please use this identifier to cite or link to this item: http://hdl.handle.net/2440/119906
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dc.contributor.authorForde, B.M.en
dc.contributor.authorMcAllister, L.J.en
dc.contributor.authorPaton, J.C.en
dc.contributor.authorPaton, A.W.en
dc.contributor.authorBeatson, S.A.en
dc.date.issued2019en
dc.identifier.citationScientific Reports, 2019; 9(1):9436-1-9436-11en
dc.identifier.issn2045-2322en
dc.identifier.issn2045-2322en
dc.identifier.urihttp://hdl.handle.net/2440/119906-
dc.description.abstractIn 1995 a severe haemolytic-uremic syndrome (HUS) outbreak in Adelaide occurred. A recent genomic analysis of Shiga toxigenic Escherichia coli (STEC) O111:H- strains 95JB1 and 95NR1 from this outbreak found that the more virulent isolate, 95NR1, harboured two additional copies of the Shiga toxin 2 (Stx2) genes encoded within prophage regions. The structure of the Stx2-converting prophages could not be fully resolved using short-read sequence data alone and it was not clear if there were other genomic differences between 95JB1 and 95NR1. In this study we have used Pacific Biosciences (PacBio) single molecule real-time (SMRT) sequencing to characterise the genome and methylome of 95JB1 and 95NR1. We completely resolved the structure of all prophages including two, tandemly inserted, Stx2-converting prophages in 95NR1 that were absent from 95JB1. Furthermore we defined all insertion sequences and found an additional IS1203 element in the chromosome of 95JB1. Our analysis of the methylome of 95NR1 and 95JB1 identified hemi-methylation of a novel motif (5'-CTGCm6AG-3') in more than 4000 sites in the 95NR1 genome. These sites were entirely unmethylated in the 95JB1 genome, and included at least 177 potential promoter regions that could contribute to regulatory differences between the strains. IS1203 mediated deactivation of a novel type IIG methyltransferase in 95JB1 is the likely cause of the observed differential patterns of methylation between 95NR1 and 95JB1. This study demonstrates the capability of PacBio SMRT sequencing to resolve complex prophage regions and reveal the genetic and epigenetic heterogeneity within a clonal population of bacteria.en
dc.description.statementofresponsibilityBrian M. Forde, Lauren J. McAllister, James C. Paton, Adrienne W. Paton and Scott A. Beatsonen
dc.language.isoenen
dc.publisherNature Publishing Groupen
dc.rights© The Author(s) 2019. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.en
dc.titleSMRT sequencing reveals differential patterns of methylation in two O111:H- STEC isolates from a hemolytic uremic syndrome outbreak in Australiaen
dc.typeJournal articleen
dc.identifier.rmid0030119487en
dc.identifier.doi10.1038/s41598-019-45760-5en
dc.relation.granthttp://purl.org/au-research/grants/nhmrc/1090456en
dc.relation.granthttp://purl.org/au-research/grants/arc/DP170103962en
dc.identifier.pubid479067-
pubs.library.collectionEnvironment Institute publicationsen
pubs.library.teamDS10en
pubs.verification-statusVerifieden
pubs.publication-statusPublisheden
dc.identifier.orcidPaton, J.C. [0000-0001-9807-5278]en
Appears in Collections:Environment Institute Leaders publications

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