{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,11]],"date-time":"2026-06-11T00:48:26Z","timestamp":1781138906386,"version":"3.54.1"},"reference-count":33,"publisher":"Microbiology Society","issue":"4","license":[{"start":{"date-parts":[[2020,4,1]],"date-time":"2020-04-01T00:00:00Z","timestamp":1585699200000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001804","name":"Canada Research Chairs","doi-asserted-by":"crossref","award":["950-228996"],"award-info":[{"award-number":["950-228996"]}],"id":[{"id":"10.13039\/501100001804","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000032","name":"Institute of Infection and Immunity","doi-asserted-by":"crossref","award":["240601"],"award-info":[{"award-number":["240601"]}],"id":[{"id":"10.13039\/501100000032","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,4,1]]},"abstract":"\n \n \n Haemophilus influenzae<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>\n causes common and sometimes severe adult and pediatric disease including chronic obstructive respiratory disease, otitis media and infections of the central nervous system. Serotype b strains, with a b-type capsule, have been the historical cause of invasive disease, and the introduction of a serotype b-specific vaccine has led to their decline. However, unencapsulated or non-b-type\n \n \n H. influenzae<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>\n infections are not prevented by the vaccine and appear to be increasing in frequency. Here we report two pediatric cases of severe central nervous system\n \n \n H. influenzae<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>\n infection presenting to the same hospital in San Diego, California during the same week in January 2016. Due to good vaccine coverage in this part of the world,\n \n \n H. influenzae<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>\n cases are normally rare and seeing two cases in the same week was unexpected. We thus suspected a recent transmission chain, and possible local outbreak. To test this hypothesis, we isolated and sequenced whole genomes from each patient and placed them in a phylogenetic tree spanning the known diversity of\n \n \n H. influenzae<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>\n . Surprisingly, we found that the two isolates (SD2016_1 and SD2016_2) belonged to distantly related lineages, suggesting two independent transmission events and ruling out a local outbreak. Despite being distantly related, the two isolates belong to two different lineages that have exchanged capsule loci in the recent past. Therefore, as in other bacterial pathogens, capsule switching by horizontal gene transfer may be an important evolutionary mechanism of vaccine evasion in\n \n \n H. influenzae<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>\n .\n <\/jats:p>","DOI":"10.1099\/mgen.0.000348","type":"journal-article","created":{"date-parts":[[2020,3,26]],"date-time":"2020-03-26T14:16:46Z","timestamp":1585232206000},"source":"Crossref","is-referenced-by-count":5,"title":["Two cases of type-a Haemophilus influenzae meningitis within the same week in the same hospital are phylogenetically unrelated but recently exchanged capsule genes"],"prefix":"10.1099","volume":"6","author":[{"given":"Yves","family":"Terrat","sequence":"first","affiliation":[{"name":"D\u00e9partement de sciences biologiques, Universit\u00e9 de Montr\u00e9al, Montr\u00e9al, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8569-4771","authenticated-orcid":false,"given":"Lauge","family":"Farnaes","sequence":"additional","affiliation":[{"name":"Rady Children's Hospital, University of California San Diego, La Jolla, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John","family":"Bradley","sequence":"additional","affiliation":[{"name":"Rady Children's Hospital, University of California San Diego, La Jolla, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4332-8463","authenticated-orcid":false,"given":"Nicolas","family":"Tromas","sequence":"additional","affiliation":[{"name":"D\u00e9partement de sciences biologiques, Universit\u00e9 de Montr\u00e9al, Montr\u00e9al, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6819-8699","authenticated-orcid":false,"given":"B. Jesse","family":"Shapiro","sequence":"additional","affiliation":[{"name":"D\u00e9partement de sciences biologiques, Universit\u00e9 de Montr\u00e9al, Montr\u00e9al, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"345","reference":[{"key":"R1","doi-asserted-by":"publisher","DOI":"10.1084\/jem.53.4.471"},{"key":"R2","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.13.2.302"},{"key":"R3","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/cix234"},{"key":"R4","doi-asserted-by":"publisher","DOI":"10.1097\/INF.0000000000001758"},{"key":"R5","doi-asserted-by":"publisher","DOI":"10.3201\/eid1805.111738"},{"key":"R6","doi-asserted-by":"publisher","DOI":"10.1016\/j.vaccine.2017.06.001"},{"key":"R7","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijid.2017.09.016"},{"key":"R8","article-title":"Global epidemiology of invasive Haemophilus influenzae type a disease: do we need a new vaccine?","volume":"14","author":"Ulanova","year":"2013","journal-title":"J Vaccines"},{"key":"R9","doi-asserted-by":"publisher","DOI":"10.1111\/j.1469-0691.2010.03417.x"},{"key":"R10","doi-asserted-by":"publisher","DOI":"10.1097\/QCO.0b013e32835310a4"},{"key":"R11","first-page":"104","article-title":"Neonatal meningitis due to non-encapsulated Haemophilus influenzae in a set of twins: A case report","volume":"35","author":"Lim","year":"1994","journal-title":"Singapore Med J"},{"key":"R12","doi-asserted-by":"publisher","DOI":"10.2147\/COPD.S15417"},{"key":"R13","doi-asserted-by":"publisher","DOI":"10.1093\/gbe\/evv062"},{"key":"R14","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msx173"},{"key":"R15","doi-asserted-by":"publisher","DOI":"10.1038\/srep44442"},{"key":"R16","doi-asserted-by":"publisher","DOI":"10.1111\/j.1558-5646.2009.00658.x"},{"key":"R17","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2008.93"},{"key":"R18","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1403353111"},{"key":"R19","doi-asserted-by":"publisher","DOI":"10.1016\/0092-8674(88)90155-9"},{"key":"R20","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.85.20.7758"},{"key":"R21","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00190-19"},{"key":"R22","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu170"},{"key":"R23","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts174"},{"key":"R24","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-9-75"},{"key":"R25","doi-asserted-by":"crossref","first-page":"3691","DOI":"10.1093\/bioinformatics\/btv421","article-title":"Roary: rapid large-scale prokaryote pan genome analysis","volume":"31","author":"Page","year":"2015","journal-title":"Bioinformatics"},{"key":"R26","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT multiple sequence alignment software version 7: improvements in performance and usability","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol Biol Evol"},{"key":"R27","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msp077"},{"key":"R28","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts386"},{"key":"R29","doi-asserted-by":"publisher","DOI":"10.1101\/gr.1239303"},{"key":"R30","doi-asserted-by":"publisher","DOI":"10.1128\/genomeA.00470-13"},{"key":"R31","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1007862"},{"key":"R32","doi-asserted-by":"publisher","DOI":"10.1016\/j.cmi.2018.10.011"},{"key":"R33","doi-asserted-by":"publisher","DOI":"10.3109\/00365548.2011.589079"}],"container-title":["Microbial Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/mgen\/10.1099\/mgen.0.000348?crawler=true&mimetype=application\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,12,14]],"date-time":"2023-12-14T21:25:23Z","timestamp":1702589123000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/mgen\/10.1099\/mgen.0.000348"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,4,1]]},"references-count":33,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2020,4,1]]}},"URL":"https:\/\/doi.org\/10.1099\/mgen.0.000348","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/619502","asserted-by":"object"}]},"ISSN":["2057-5858"],"issn-type":[{"value":"2057-5858","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,4,1]]}}}