{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,8]],"date-time":"2026-10-08T06:18:19Z","timestamp":1791440299006,"version":"4.3.3"},"reference-count":64,"publisher":"Microbiology Society","issue":"2","license":[{"start":{"date-parts":[[2022,2,23]],"date-time":"2022-02-23T00:00:00Z","timestamp":1645574400000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,2,23]]},"abstract":"Bacterial genetic diversity is often described solely using base-pair changes despite a wide variety of other mutation types likely being major contributors. Tandem duplication\/amplifications are thought to be widespread among bacteria but due to their often-intractable size and instability, comprehensive studies of these mutations are rare. We define a methodology to investigate amplifications in bacterial genomes based on read depth of genome sequence data as a proxy for copy number. We demonstrate the approach with \n \n Bordetella pertussis<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>, whose insertion sequence element-rich genome provides extensive scope for amplifications to occur. Analysis of data for 2430 \n \n B. pertussis<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> isolates identified 272 putative amplifications, of which 94\u200a% were located at 11 hotspot loci. We demonstrate limited phylogenetic connection for the occurrence of amplifications, suggesting unstable and sporadic characteristics. Genome instability was further described in vitro<\/jats:italic> using long-read sequencing via the Nanopore platform, which revealed that clonally derived laboratory cultures produced heterogenous populations rapidly. We extended this research to analyse a population of 1000 isolates of another important pathogen, \n \n Mycobacterium tuberculosis<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>. We found 590 amplifications in \n \n M. tuberculosis<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>, and like \n \n B. pertussis<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>, these occurred primarily at hotspots. Genes amplified in \n \n B. pertussis<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> include those involved in motility and respiration, whilst in M. tuberuclosis<\/jats:italic>, functions included intracellular growth and regulation of virulence. Using publicly available short-read data we predicted previously unrecognized, large amplifications in \n \n B. pertussis<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> and \n \n M. tuberculosis<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>. This reveals the unrecognized and dynamic genetic diversity of \n \n B. pertussis<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> and \n \n M. tuberculosis<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>, highlighting the need for a more holistic understanding of bacterial genetics.<\/jats:p>","DOI":"10.1099\/mgen.0.000761","type":"journal-article","created":{"date-parts":[[2022,2,10]],"date-time":"2022-02-10T18:16:02Z","timestamp":1644516962000},"source":"Crossref","is-referenced-by-count":3,"title":["Towards comprehensive understanding of bacterial genetic diversity: large-scale amplifications in Bordetella pertussis and Mycobacterium tuberculosis"],"prefix":"10.1099","volume":"8","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5122-4691","authenticated-orcid":false,"given":"Jonathan S.","family":"Abrahams","sequence":"first","affiliation":[{"name":"Department of Biology and Biochemistry and Milner Centre for Evolution, University of Bath, Bath, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7278-0160","authenticated-orcid":false,"given":"Michael R.","family":"Weigand","sequence":"additional","affiliation":[{"name":"Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8971-8507","authenticated-orcid":false,"given":"Natalie","family":"Ring","sequence":"additional","affiliation":[{"name":"Department of Biology and Biochemistry and Milner Centre for Evolution, University of Bath, Bath, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4855-6484","authenticated-orcid":false,"given":"Iain","family":"MacArthur","sequence":"additional","affiliation":[{"name":"Department of Biology and Biochemistry and Milner Centre for Evolution, University of Bath, Bath, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0480-5968","authenticated-orcid":false,"given":"Joss","family":"Etty","sequence":"additional","affiliation":[{"name":"Department of Biology and Biochemistry and Milner Centre for Evolution, University of Bath, Bath, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Scott","family":"Peng","sequence":"additional","affiliation":[{"name":"Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Margaret M.","family":"Williams","sequence":"additional","affiliation":[{"name":"Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Barret","family":"Bready","sequence":"additional","affiliation":[{"name":"Nabsys 2.0, Providence, RI 02809, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1312-0696","authenticated-orcid":false,"given":"Anthony P.","family":"Catalano","sequence":"additional","affiliation":[{"name":"Nabsys 2.0, Providence, RI 02809, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jennifer R.","family":"Davis","sequence":"additional","affiliation":[{"name":"Nabsys 2.0, Providence, RI 02809, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0839-7351","authenticated-orcid":false,"given":"Michael D.","family":"Kaiser","sequence":"additional","affiliation":[{"name":"Nabsys 2.0, Providence, RI 02809, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5489-0737","authenticated-orcid":false,"given":"John S.","family":"Oliver","sequence":"additional","affiliation":[{"name":"Nabsys 2.0, Providence, RI 02809, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jay M.","family":"Sage","sequence":"additional","affiliation":[{"name":"Nabsys 2.0, Providence, RI 02809, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2302-9511","authenticated-orcid":false,"given":"Stefan","family":"Bagby","sequence":"additional","affiliation":[{"name":"Department of Biology and Biochemistry and Milner Centre for Evolution, University of Bath, Bath, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M. Lucia","family":"Tondella","sequence":"additional","affiliation":[{"name":"Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2193-7954","authenticated-orcid":false,"given":"Andrew R.","family":"Gorringe","sequence":"additional","affiliation":[{"name":"Public Health England, Porton Down, Salisbury, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew","family":"Preston","sequence":"additional","affiliation":[{"name":"Department of Biology and Biochemistry and Milner Centre for Evolution, University of Bath, Bath, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"345","reference":[{"key":"R1","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-018-0342-0"},{"key":"R2","doi-asserted-by":"publisher","DOI":"10.1111\/mmi.13459"},{"key":"R3","article-title":"Multiple capsule genes in H. influenzae","volume":"192","author":"Cerquetti","year":"2005","journal-title":"JID"},{"key":"R4","doi-asserted-by":"publisher","DOI":"10.1016\/0092-8674(83)90228-3"},{"key":"R5","doi-asserted-by":"publisher","DOI":"10.1038\/ng1227"},{"key":"R6","doi-asserted-by":"publisher","DOI":"10.1080\/22221751.2019.1587315"},{"key":"R7","doi-asserted-by":"publisher","DOI":"10.1128\/JB.00806-16"},{"key":"R8","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-11-64"},{"key":"R9","doi-asserted-by":"publisher","DOI":"10.1186\/1756-0500-7-727"},{"key":"R10","doi-asserted-by":"publisher","DOI":"10.1128\/genomeA.00973-17"},{"key":"R11","doi-asserted-by":"publisher","DOI":"10.1080\/15476286.2018.1462655"},{"key":"R12","article-title":"Significant gene order and expression differences in Bordetella pertussis despite limited gene content variation","volume":"188","author":"Brinig","year":"2020","journal-title":"J Bacteriol"},{"key":"R13","doi-asserted-by":"publisher","DOI":"10.1093\/femspd\/fty071"},{"key":"R14","doi-asserted-by":"publisher","DOI":"10.1016\/j.micinf.2006.04.014"},{"key":"R15","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.72.8.4874-4877.2004"},{"key":"R16","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0000904"},{"key":"R17","doi-asserted-by":"publisher","DOI":"10.1128\/genomeA.01404-16"},{"key":"R18","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.00869-17"},{"key":"R19","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000234"},{"key":"R20","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.16.3.463-496.2003"},{"key":"R21","doi-asserted-by":"publisher","DOI":"10.1186\/s13073-019-0660-8"},{"key":"R22","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.00969-16"},{"key":"R23","doi-asserted-by":"publisher","DOI":"10.1038\/31159"},{"key":"R24","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.01791-14"},{"key":"R25","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0026038"},{"key":"R26","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0700869104"},{"key":"R27","doi-asserted-by":"publisher","DOI":"10.2807\/1560-7917.ES2014.19.33.20881"},{"key":"R28","article-title":"Aligning sequence reads, clone sequences and assembly contigs with bwa-membwa-mem","author":"Li","year":"2013","journal-title":"arXiv"},{"key":"R29","doi-asserted-by":"publisher","DOI":"10.1101\/gr.114876.110"},{"key":"R30","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btr708"},{"key":"R31","doi-asserted-by":"publisher","DOI":"10.1128\/mSphere.00036-16"},{"key":"R32","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.00869-17"},{"key":"R33","article-title":"The igraph software package for complex network research","volume":"1695","author":"Csardi","year":"2006","journal-title":"InterJournal Complex Systems"},{"key":"R34","doi-asserted-by":"publisher","DOI":"10.1002\/spe.4380211102"},{"key":"R35","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msaa015"},{"key":"R36","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msx281"},{"key":"R37","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/mst024"},{"key":"R38","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4285"},{"key":"R39","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btl529"},{"key":"R40","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-15-467"},{"key":"R41","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.2198"},{"key":"R42","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1007069"},{"key":"R43","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.00869-17"},{"key":"R44","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-genet-102108-134805"},{"key":"R45","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1993.1488"},{"key":"R46","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(15)00062-6"},{"key":"R47","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1000767"},{"key":"R48","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0504922102"},{"key":"R49","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2958.2010.07463.x"},{"key":"R50","doi-asserted-by":"publisher","DOI":"10.1128\/genomeA.01080-16"},{"key":"R51","doi-asserted-by":"publisher","DOI":"10.1128\/mSystems.00702-19"},{"key":"R52","doi-asserted-by":"publisher","DOI":"10.1007\/s10709-008-9289-z"},{"key":"R53","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.78.5.3113"},{"key":"R54","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/jiy125"},{"key":"R55","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.00787-19"},{"key":"R56","doi-asserted-by":"publisher","DOI":"10.1007\/BF00330301"},{"key":"R57","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gks778"},{"key":"R58","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gki954"},{"key":"R59","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0053486"},{"key":"R60","doi-asserted-by":"publisher","DOI":"10.1128\/jb.179.9.2922-2929.1997"},{"key":"R61","doi-asserted-by":"publisher","DOI":"10.1006\/mpat.2001.0431"},{"key":"R62","doi-asserted-by":"publisher","DOI":"10.1099\/mic.0.000578"},{"key":"R63","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.71.12.7170-7172.2003"},{"key":"R64","doi-asserted-by":"publisher","DOI":"10.1016\/j.meegid.2009.10.007"}],"container-title":["Microbial Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/mgen\/10.1099\/mgen.0.000761?crawler=true&mimetype=application\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,12,14]],"date-time":"2023-12-14T21:22:42Z","timestamp":1702588962000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/mgen\/10.1099\/mgen.0.000761"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,2,23]]},"references-count":64,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2022,2,23]]}},"URL":"https:\/\/doi.org\/10.1099\/mgen.0.000761","relation":{},"ISSN":["2057-5858"],"issn-type":[{"value":"2057-5858","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,2,23]]}}}