Whole-genome comparison of two Campylobacter jejuni isolates of the same sequence type reveals multiple loci of different ancestral lineage
Campylobacter jejuni ST-474 is the most important human enteric pathogen in New Zealand, and yet this genotype is rarely found elsewhere in the world. Insight into the evolution of this organism was gained by a whole genome comparison of two ST-474, flaA SVR-14 isolates and other available C. jejuni...
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| description | Campylobacter jejuni ST-474 is the most important human enteric pathogen in New Zealand, and yet this genotype is rarely found elsewhere in the world. Insight into the evolution of this organism was gained by a whole genome comparison of two ST-474, flaA SVR-14 isolates and other available C. jejuni isolates and genomes. The two isolates were collected from different sources, human (H22082) and retail poultry (P110b), at the same time and from the same geographical location. Solexa sequencing of each isolate resulted in ~1.659 Mb (H22082) and ~1.656 Mb (P110b) of assembled sequences within 28 (H22082) and 29 (P110b) contigs. We analysed 1502 genes for which we had sequences within both ST-474 isolates and within at least one of 11 C. jejuni reference genomes. Although 94.5% of genes were identical between the two ST-474 isolates, we identified 83 genes that differed by at least one nucleotide, including 55 genes with non-synonymous substitutions. These covered 101 kb and contained 672 point differences. We inferred that 22 (3.3%) of these differences were due to mutation and 650 (96.7%) were imported via recombination. Our analysis estimated 38 recombinant breakpoints within these 83 genes, which correspond to recombination events affecting at least 19 loci regions and gives a tract length estimate of ~2 kb. This includes a ~12 kb region displaying non-homologous recombination in one of the ST-474 genomes, with the insertion of two genes, including ykgC, a putative oxidoreductase, and a conserved hypothetical protein of unknown function. Furthermore, our analysis indicates that the source of this recombined DNA is more likely to have come from C. jejuni strains that are more closely related to ST-474. This suggests that the rates of recombination and mutation are similar in order of magnitude, but that recombination has been much more important for generating divergence between the two ST-474 isolates. |
| doi_str_mv | 10.1371/journal.pone.0027121 |
| format | Article |
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Insight into the evolution of this organism was gained by a whole genome comparison of two ST-474, flaA SVR-14 isolates and other available C. jejuni isolates and genomes. The two isolates were collected from different sources, human (H22082) and retail poultry (P110b), at the same time and from the same geographical location. Solexa sequencing of each isolate resulted in ~1.659 Mb (H22082) and ~1.656 Mb (P110b) of assembled sequences within 28 (H22082) and 29 (P110b) contigs. We analysed 1502 genes for which we had sequences within both ST-474 isolates and within at least one of 11 C. jejuni reference genomes. Although 94.5% of genes were identical between the two ST-474 isolates, we identified 83 genes that differed by at least one nucleotide, including 55 genes with non-synonymous substitutions. These covered 101 kb and contained 672 point differences. We inferred that 22 (3.3%) of these differences were due to mutation and 650 (96.7%) were imported via recombination. Our analysis estimated 38 recombinant breakpoints within these 83 genes, which correspond to recombination events affecting at least 19 loci regions and gives a tract length estimate of ~2 kb. This includes a ~12 kb region displaying non-homologous recombination in one of the ST-474 genomes, with the insertion of two genes, including ykgC, a putative oxidoreductase, and a conserved hypothetical protein of unknown function. Furthermore, our analysis indicates that the source of this recombined DNA is more likely to have come from C. jejuni strains that are more closely related to ST-474. This suggests that the rates of recombination and mutation are similar in order of magnitude, but that recombination has been much more important for generating divergence between the two ST-474 isolates.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0027121</identifier><identifier>PMID: 22096527</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Bacterial genetics ; Biology ; Biotechnology ; Breakpoints ; Campylobacter ; Campylobacter coli ; Campylobacter jejuni ; Campylobacter jejuni - classification ; Campylobacter jejuni - genetics ; Deoxyribonucleic acid ; Divergence ; DNA ; DNA sequencing ; E coli ; Escherichia coli ; Ethics ; Evolution ; FlaA protein ; Gene sequencing ; Genes ; Genetic aspects ; Genetic diversity ; Genome, Bacterial - genetics ; Genomes ; Genomics ; Geographical distribution ; Health surveillance ; Homologous recombination ; Homologous Recombination - genetics ; Homology ; Loci ; Medicine ; Mutation ; Nucleotide sequence ; Oxidoreductase ; Pathogens ; Physics ; Poultry ; Public health ; Recombination, Genetic - genetics ; Surveillance ; Zoonoses</subject><ispartof>PloS one, 2011-11, Vol.6 (11), p.e27121-e27121</ispartof><rights>COPYRIGHT 2011 Public Library of Science</rights><rights>2011 Biggs et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: https://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>Biggs et al. 2011</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c691t-dc7f6569c7989d7dbca824aa696e3af6998fad88f2007b0932922d6145a58e353</citedby></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3214069/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3214069/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23845,27901,27902,53766,53768,79342,79343</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/22096527$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Biggs, Patrick J</creatorcontrib><creatorcontrib>Fearnhead, Paul</creatorcontrib><creatorcontrib>Hotter, Grant</creatorcontrib><creatorcontrib>Mohan, Vathsala</creatorcontrib><creatorcontrib>Collins-Emerson, Julie</creatorcontrib><creatorcontrib>Kwan, Errol</creatorcontrib><creatorcontrib>Besser, Thomas E</creatorcontrib><creatorcontrib>Cookson, Adrian</creatorcontrib><creatorcontrib>Carter, Philip E</creatorcontrib><creatorcontrib>French, Nigel P</creatorcontrib><title>Whole-genome comparison of two Campylobacter jejuni isolates of the same sequence type reveals multiple loci of different ancestral lineage</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Campylobacter jejuni ST-474 is the most important human enteric pathogen in New Zealand, and yet this genotype is rarely found elsewhere in the world. Insight into the evolution of this organism was gained by a whole genome comparison of two ST-474, flaA SVR-14 isolates and other available C. jejuni isolates and genomes. The two isolates were collected from different sources, human (H22082) and retail poultry (P110b), at the same time and from the same geographical location. Solexa sequencing of each isolate resulted in ~1.659 Mb (H22082) and ~1.656 Mb (P110b) of assembled sequences within 28 (H22082) and 29 (P110b) contigs. We analysed 1502 genes for which we had sequences within both ST-474 isolates and within at least one of 11 C. jejuni reference genomes. Although 94.5% of genes were identical between the two ST-474 isolates, we identified 83 genes that differed by at least one nucleotide, including 55 genes with non-synonymous substitutions. These covered 101 kb and contained 672 point differences. We inferred that 22 (3.3%) of these differences were due to mutation and 650 (96.7%) were imported via recombination. Our analysis estimated 38 recombinant breakpoints within these 83 genes, which correspond to recombination events affecting at least 19 loci regions and gives a tract length estimate of ~2 kb. This includes a ~12 kb region displaying non-homologous recombination in one of the ST-474 genomes, with the insertion of two genes, including ykgC, a putative oxidoreductase, and a conserved hypothetical protein of unknown function. Furthermore, our analysis indicates that the source of this recombined DNA is more likely to have come from C. jejuni strains that are more closely related to ST-474. This suggests that the rates of recombination and mutation are similar in order of magnitude, but that recombination has been much more important for generating divergence between the two ST-474 isolates.</description><subject>Bacterial genetics</subject><subject>Biology</subject><subject>Biotechnology</subject><subject>Breakpoints</subject><subject>Campylobacter</subject><subject>Campylobacter coli</subject><subject>Campylobacter jejuni</subject><subject>Campylobacter jejuni - classification</subject><subject>Campylobacter jejuni - genetics</subject><subject>Deoxyribonucleic acid</subject><subject>Divergence</subject><subject>DNA</subject><subject>DNA sequencing</subject><subject>E coli</subject><subject>Escherichia coli</subject><subject>Ethics</subject><subject>Evolution</subject><subject>FlaA protein</subject><subject>Gene sequencing</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Genetic diversity</subject><subject>Genome, Bacterial - genetics</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Geographical distribution</subject><subject>Health surveillance</subject><subject>Homologous recombination</subject><subject>Homologous Recombination - genetics</subject><subject>Homology</subject><subject>Loci</subject><subject>Medicine</subject><subject>Mutation</subject><subject>Nucleotide sequence</subject><subject>Oxidoreductase</subject><subject>Pathogens</subject><subject>Physics</subject><subject>Poultry</subject><subject>Public health</subject><subject>Recombination, Genetic - genetics</subject><subject>Surveillance</subject><subject>Zoonoses</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2011</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><sourceid>DOA</sourceid><recordid>eNqNk9tu1DAQhiMEolB4AwSWkEBc7GI7iRPfIFUVh0qVKnG8tBxnvOuVEwfbKfQZeGlm223VRb1AuUjkfP8_B88UxTNGl6xs2NtNmOOo_XIKIywp5Q3j7F7xiMmSLwSn5f1b3wfF45Q2lNZlK8TD4oBzKkXNm0fFnx_r4GGxgjEMQEwYJh1dCiMJluRfgRzrYbrwodMmQyQb2MyjIwh4nSFdQmsgSaM2wc8ZRgMkX0xAIpyD9okMs89u8kB8MG7L985aiDBmohFOOWpPvBtBr-BJ8cCiBp7u3ofFtw_vvx5_WpyefTw5PjpdGCFZXvSmsaIW0jSylX3Td0a3vNJaSAGltkLK1uq-bS2ntOko9kBy3gtW1bpuoazLw-LFle_kQ1K7PibFSsYkbyvKkTi5IvqgN2qKbtDxQgXt1OVBiCulY3bGg-rKvjGVNBrDVhw6zMVygWl0jeg1s-j1bhdt7gboDZaONe-Z7v8Z3VqtwrkqOauokGjwemcQA7Y4ZTW4ZMB7PUKYk5K0Fg3efoPky3_Iu4vbUSuN-bvRBgxrtp7qqGpEKxClSC3voPDpYXAGZ846PN8TvNkTIJPhd17pOSV18uXz_7Nn3_fZV7fYNU5VXuP8zdmFMe2D1RVoYkgpgr3pMaNquzLX3VDblVG7lUHZ89v3cyO63pHyL0jAE6Y</recordid><startdate>20111111</startdate><enddate>20111111</enddate><creator>Biggs, Patrick J</creator><creator>Fearnhead, Paul</creator><creator>Hotter, Grant</creator><creator>Mohan, Vathsala</creator><creator>Collins-Emerson, Julie</creator><creator>Kwan, Errol</creator><creator>Besser, Thomas E</creator><creator>Cookson, Adrian</creator><creator>Carter, Philip E</creator><creator>French, Nigel P</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>IOV</scope><scope>ISR</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20111111</creationdate><title>Whole-genome comparison of two Campylobacter jejuni isolates of the same sequence type reveals multiple loci of different ancestral lineage</title><author>Biggs, Patrick J ; Fearnhead, Paul ; Hotter, Grant ; Mohan, Vathsala ; Collins-Emerson, Julie ; Kwan, Errol ; Besser, Thomas E ; Cookson, Adrian ; Carter, Philip E ; French, Nigel P</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c691t-dc7f6569c7989d7dbca824aa696e3af6998fad88f2007b0932922d6145a58e353</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2011</creationdate><topic>Bacterial genetics</topic><topic>Biology</topic><topic>Biotechnology</topic><topic>Breakpoints</topic><topic>Campylobacter</topic><topic>Campylobacter coli</topic><topic>Campylobacter jejuni</topic><topic>Campylobacter jejuni - 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Insight into the evolution of this organism was gained by a whole genome comparison of two ST-474, flaA SVR-14 isolates and other available C. jejuni isolates and genomes. The two isolates were collected from different sources, human (H22082) and retail poultry (P110b), at the same time and from the same geographical location. Solexa sequencing of each isolate resulted in ~1.659 Mb (H22082) and ~1.656 Mb (P110b) of assembled sequences within 28 (H22082) and 29 (P110b) contigs. We analysed 1502 genes for which we had sequences within both ST-474 isolates and within at least one of 11 C. jejuni reference genomes. Although 94.5% of genes were identical between the two ST-474 isolates, we identified 83 genes that differed by at least one nucleotide, including 55 genes with non-synonymous substitutions. These covered 101 kb and contained 672 point differences. We inferred that 22 (3.3%) of these differences were due to mutation and 650 (96.7%) were imported via recombination. Our analysis estimated 38 recombinant breakpoints within these 83 genes, which correspond to recombination events affecting at least 19 loci regions and gives a tract length estimate of ~2 kb. This includes a ~12 kb region displaying non-homologous recombination in one of the ST-474 genomes, with the insertion of two genes, including ykgC, a putative oxidoreductase, and a conserved hypothetical protein of unknown function. Furthermore, our analysis indicates that the source of this recombined DNA is more likely to have come from C. jejuni strains that are more closely related to ST-474. This suggests that the rates of recombination and mutation are similar in order of magnitude, but that recombination has been much more important for generating divergence between the two ST-474 isolates.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>22096527</pmid><doi>10.1371/journal.pone.0027121</doi><tpages>e27121</tpages><oa>free_for_read</oa></addata></record> |
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| source | MEDLINE; DOAJ Directory of Open Access Journals; EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry; Public Library of Science (PLoS) |
| subjects | Bacterial genetics Biology Biotechnology Breakpoints Campylobacter Campylobacter coli Campylobacter jejuni Campylobacter jejuni - classification Campylobacter jejuni - genetics Deoxyribonucleic acid Divergence DNA DNA sequencing E coli Escherichia coli Ethics Evolution FlaA protein Gene sequencing Genes Genetic aspects Genetic diversity Genome, Bacterial - genetics Genomes Genomics Geographical distribution Health surveillance Homologous recombination Homologous Recombination - genetics Homology Loci Medicine Mutation Nucleotide sequence Oxidoreductase Pathogens Physics Poultry Public health Recombination, Genetic - genetics Surveillance Zoonoses |
| title | Whole-genome comparison of two Campylobacter jejuni isolates of the same sequence type reveals multiple loci of different ancestral lineage |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-04T21%3A45%3A51IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Whole-genome%20comparison%20of%20two%20Campylobacter%20jejuni%20isolates%20of%20the%20same%20sequence%20type%20reveals%20multiple%20loci%20of%20different%20ancestral%20lineage&rft.jtitle=PloS%20one&rft.au=Biggs,%20Patrick%20J&rft.date=2011-11-11&rft.volume=6&rft.issue=11&rft.spage=e27121&rft.epage=e27121&rft.pages=e27121-e27121&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0027121&rft_dat=%3Cgale_plos_%3EA476863110%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1311928402&rft_id=info:pmid/22096527&rft_galeid=A476863110&rft_doaj_id=oai_doaj_org_article_b3d7c49ca99842eba82f26af6b76da1f&rfr_iscdi=true |