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Home , Clostridiaceae, Clostridium argentinense, Clostridium chauvoei, Clostridium novyi, Clostridium pasteurianum, Clostridium septicum

AMMI-CACMID 1,2* 3 Serial no. 0083 Emendation of the Genus and validation of ‘Clostridium neonatale’ sp. nov. as a member of that genus K.A. Bernard A-M Bernier Prog no. P15 1National Laboratory (NML), Public Health Agency of Canada, Winnipeg Manitoba (MB), Canada; 2University of Manitoba, Winnipeg MB; 3Université de Saint-Boniface, Winnipeg MB

52 Clostridium estertheticum NCIMB 12511T NR 118995 RESULTS and DISCUSSION INTRODUCTION: 79 Clostridium frigoris DSM 14204 NR 114878 38 Clostridium lacusfryxellense C/C-an/B1T NR 025558 2017 REVIEW OF THE GENUS CLOSTRIDIUM 42 Clostridium algoriphilum 14D1T NR 115146 * 47 Clostridium bowmanii A-1/C-an/C1T NR 037091 * • Genus Clostridium 1st described in 1880 by Prazmowski; is type genus of the family 100 Clostridium psychrophilum A-1/C-an/IT NR 037090 * 1. 100 species in genus Clostridium sensu 57 Clostridium tagluense A121T NR 043698 * 100 Clostridium sulfidigenes SGB2T NR 044161 * stricto, based on this review (Primbram 1933) and part of the order Clostridiales (Prévot 1953) (1, 2, 4) Clostridium thiosulfatireducens Lup21T NR 114590 * 69 Clostridium tunisiense TJT NR 115161 2. 37 validly named Clostridium species were • are Gram positive rods, strictly anaerobic, (few species aerotolerant), spore 80 100 Clostridium huakuii LAM1030T NR 134006 * 79 Clostridium punense BLPYG-8T NR 145903 * 71 Clostridium amazonense NE08VT NR 145540 * omitted in the latest emendation by Collins formers Clostridium senegalense JC122T NR 125591 * 51 Clostridium vulturis YMB-57T JQ423949 * Clostridium subterminale NCIMB 10746T NR 118999 and Rainey (2), including important • Extreme heterogeneity of genus found by 16S rRNA sequence analysis in 1994 (1) 32 30 C. botulinum 100 ATCC 27322T NR 029232 group IV • Lawson and Rainey proposed restricting genus Clostridium only to those species 86 Type G ATCC 27322 M59087 , C. perfringens [missing species 90 Clostridium schirmacherense AP15T NR 042448 * 100 Clostridium pascui DSM 10365T NR 026322 are marked with * in Fig 1] closest to the type species C. butyricum (‘Clostridium Cluster I’) in 2016 (2) Clostridium peptidivorans TMC4T NR 025019 46 DSM 17049T NR 043235 * • In 2002, short clinical paper which cited ‘C. neonatale’ was published but species novum 3065 96 Clostridium tetanomorphum DSM 4474T NR 043671 * 3. We will propose that 3 taxa from genus Clostridium liquoris BEY10T KC331197 * never validated (5) 76 Clostridium acetireducens 30AT NR 026179 Eubacterium be reassigned to genus 42 Clostridium malenominatum DSM 1127T NR 104780 47 Clostridium cochlearium JCM 1396T NR 113026 • We report here that Clostridium (Lawson and Rainey) requires further emendation after 100 NCTC 279T NR 029260 Clostridium sensu stricto (orange) Clostridium collagenovorans SGT NR 029246 Clostridium acetobutylicum ATCC 824T NR 119091 4. ‘Clostridium neonatale’ fits genus this review and that ‘C. neonatale’ best fits the emended genus as modified in 2016 13 89 100 Clostridium aurantibutyricum DSM 793T NR 116616 100 Clostridium felsineum NCIMB 10690T NR 114566* Clostridium as emended by Lawson & 99 Clostridium arbusti SL206T NR 116458 * 66 DSM 525T NR 104822 100 CK74T NR 028898 Rainey; “C.neonatale” isolates had 99.8%- METHODS: Assessing Species in the Genus Clostridium Clostridium akagii CK58T NR 025352 * 64 SL1T NR 044942 100% identity to each other but < 98.0% 100 Clostridium scatologenes ATCC 25775T NR 118727 48 46 Clostridium carboxidivorans P7T NR 104768 identity to other species on tree (red, ref 5) 2 68 Clostridium magnum DSM 2767 NR 119084 • Clostridium species in the List of Prokaryotes with Standing in Nomenclature (LSPN, Clostridium aciditolerans JW/YJL-B3T NR 043557 * 100 Clostridium nitrophenolicum 1DT NR 042516 * 5. 3 taxa have internet presence but are not http:// www.bacterio.net/ clostridium. html (April 2017)), Bergey’s Clostridium chapter (4) 52 Clostridium kogasensis YHK0403T NR 136452 89 Clostridium algifaecis MB9-7 NR 134004 * validly named (purple) or IJSEM publications, were independently reviewed for relationship to Cluster I bacteria 21 Clostridium tyrobutyricum ATCC 25755TNR 044718 99 DSM 13528T NR 117113 49 DSM 555T NR 074165 • Newer Clostridium species were considered only if published in IJSEM as a species 85 Clostridium luticellarii FW431T NR 145907 * UPDATE-Clostridium species belonging to other Clostridium swellfunianum S11-3-10T NR 126179 * novum or were cited in an IJSB / IJSEM ‘List’ (any year up to 2017) 16 Clostridium bornimense M2/40T NR 134005 * ‘Clostridiales Clusters” (1, 4); handout available on 37 Clostridium oryzae KC3T NR 124714 * 28 Clostridium (formerly ) polyendosporus PS-1T NR 026496 UM website, link below] • Newer Clostridium species were also assessed for being consistent with and if included Clostridium algidicarnis NCFB 2931T NR 041746 15 15 100 Clostridium putrefaciens DSM 1291T NR 119282 in, the emended Clostridium genus description by Lawson and Rainey (2) 14 Clostridium amylolyticum SW408T NR 044386 * 14 100 Clostridium polynesiense MS1T NR 144690 - Most still called Clostridium species; all will Catt39T NR 029263 • Taxa historically assigned to other genera which appeared to best fit the emended 3 Clostridium fallax ATCC 19400T NR 044714 Clostridium cavendishii BL-28T NR 115711 * be reassigned to new genera in the future. Clostridium genus but possibly omitted from ref 2, also reviewed 639 Clostridium cellulovorans 743BT NR 102875 * JCM 1392T NR 104695 - Most recent addition to any cluster was 2009 ‘Clostridium neonatale’ Review: 47 Clostridium frigidicarnis SPL77AT NR 024919 99 Clostridium hydrogeniformans BL-20T NR 115712 * Cluster II: 3 species assigned to genus 100 2585T NR 026013 • “C. neonatale” was first recovered from an outbreak of necrotizing enterocolitis (NEC) 60 ATCC 12464T NR 026020 42 Clostridium carnis ATCC 25777T NR 044716 Hathewaya (2) • “Clostridium neonatale” clinical features were first described by Alfa et al in 2002 (ref 3) 88 Clostridium isatidis WV6T NR 026347 * Clostridium sartagoforme DSM 1292T NR 026490 Cluster III: 15 Clostridium species; none as yet 6262 JCM 6289T NR 113325 • “C. neonatale” microbiological features were cited in brief in clinical paper but were NOT 29 Clostridium quinii DSM 6736T NR 026149 2298 DSM 1785T NR 026167 reassigned to new genera formally described/validated at that time 99 DS1T NR 026491 Clostridium (Eubacterium) tarantellae UM-87T NR 104741 Cluster IV: 5 species, 4 not as yet reassigned • “C. neonatale” microbiological features have been recently revisited as part of exercise 87 Clostridium () maximum DSM 316T NR 026147 100 Clostridium (Sarcina) ventriculi DSM 286T NR 026146 Cluster V: 2 species assigned to genus 56 Eubacterium budayi JCM 9989T NR 024682 to finally validly describe this organism (2017 ECCMID, ref 5) 93 Eubacterium nitritogenes JCM 6485T NR 024684 83 18 IP 2227T NR 029229 Thermanaerobacter (1) • “C. neonatale” has been recovered in at least France and several studies involving a 58 100 Clostridium sardiniense DSM 2632T NR 112226 55 Clostridium (Eubacterium) moniliforme JCM 9990T NR 113037 Cluster VI: 2 species assigned to genus reference strain (NML 99A005T) had been published 23 3WC2T NR 028964 JCM 1290T NR 113204 * Clostridium botulinum type E (Iwanai) X68170 C. botulinum Moorella (1) 100 • Characteristics of “Clostridium neonatale” have been summarized, including Clostridium botulinum Type F (Eklund 202F ATCC 23387) group II 87 Clostridium botulinum Type B (Eklund 17B ATCC 25765) Cluster VII: 2 species assigned to genus biochemical, cellular fatty acids, AST, 16S rRNA gene sequencing and whole genome 2011 CK55T NR 028920 * 7 Clostridium gasigenes DSM 12272T NR 024945 Clostridium paraputrificum JCM 1293T NR 113021 Thermoanaerobacterium (1) sequencing of 2 reference strains (99A005T and 99A006) (5) 45 Clostridium vincentii DSM 10228T NR 026336 8 Clostridium chartatabidum 163T NR 029239 Cluster IX: 1 species assigned to genus 3 Clostridium neonatale NML99-A-005T AF275949 REFERENCES CITED 55 JCM 1391T NR 113244 (Type Species) Dendrosporobacter 56 Clostridium chromiireducens GCAF-1T NR 122090 * 1. Collins, Lawson, Willems et al. 1994. Phylogeny of the Genus Clostridium: proposal of five new Genera and 74 Clostridium saccharobutylicum NCP 262T NR 121710 Cluster XI: 19 species of which 9 have been 22 Clostridium puniceum BL 70/20T NR 026105 Eleven new species combinations. IJSEM 44: 812-826 99 45 Clostridium saccharoperbutylacetonicum N1-4(HMT)T NR 102516 64 JCM 1390T NR 113388 assigned to 7 genera, including genus 2. Lawson and Rainey. 2016 Proposal to restrict the genus Clostridium Prazmowski to Clostridium butyricum 99 SH1T NR 025542 * Clostridium roseum strain 653T NR 029354 ‘Clostridioides’ for C. difficile (6). and related species. IJSEM 66: 1009-1016 97 Clostridium aestuarii HY-45-18T NR 043569 * 74 HY-42-06T NR 043266 * 3. Alfa, M., D. Robson, M. Davi, K. Bernard, P. VanCaeseele, G.K. Harding. 2002 CID 35 (suppl 1) S101-S105. A1T NR 026131 Cluster XII: 2 species, not yet reassigned Clostridium homopropionicum DSM 5847T NR 026148 AL 98 4. Rainey, F. A., B. J. Hollen; A. Small. 2008 Genus 1. Clostridium Prazmowski 1880, 23 in Bergey's Manual 99 Clostridium thermobutyricum JW171KT NR 044849 Cluster XIVa: 32 species, of which 3 species 57 Clostridium thermopalmarium BVPT NR 026112 of Systematic Bacteriology 2nd ed. Pg 738-828, Springer NY 75 JCM 1406T NR 113022 have been assigned to 3 genera. Cluster 100 Clostridium botulinum type D NCTC 8265 X68187 C. botulinum 5. Bernard, K. A. & A-M. Bernier. 2017. Revisiting ‘Clostridium neonatale’: delineating an effective description 97 Clostridium botulinum type C Strain 468 X68315 group III 92 Clostridium haemolyticum DSM 5565T NR 119281 includes family Lachnospiraceae genera as preamble for inclusion In the genus Clostridium sensu stricto as Clostridium neonatale sp. nov. ECCMID Clostridium tepidiprofundi SG 508T NR 044159 * 43 Clostridium oceanicum DSM 1290T NR 117136 Cluster XIVb: 5 species , 1 of which has been April 22, 2017, Vienna Austria, E-Poster reference no. 2849. 99 ATCC 3584T NR 029231 Eubacterium combesii ATCC 25545T NR 042951 100 C. botulinum reassigned to new genus. 6. Lawson, P.A.; D. M. Citron; K.L. Tyrrell; S. M. Finegold. 2016. Reclassification of Clostridium difficile as 59 Clostridium botulinum type A ELTDK 103 (ATCC 25763T) NR 029157 59 53 Clostridium botulinum Type B NCTC 7273 X68186 group I Clostridioides difficile (Hall and O’Toole 1935) Prévot 1938. Anaerobe 40:95-99 [not as yet validated ] Clostridium botulinum Type F ATCC 25764 L37593 Cluster XV: 1 species reassigned to 47 Hathewaya (Clostridium) histolytica JCM 1403T NR 113187 [Hathewaya= Cluster II] Hathewaya (Clostridium) limosa CECT 4329T NR 104825 CONTACT Kathryn Bernard 100 Hathawaya (Clostridium) proteolytica CGT NR 029250 Eubacterium as E. barkeri (1) Acknowledgements: ‘Clostridioides’ (Clostridium) difficile ATCC 9689T NR 112172 [Cluster XI] We thank: National Microbiology Laboratory, Public Health Agency of Atopobium parvulum JCM 10300T NR 113159 [unrelated outgroup] Cluster XVI: 1 species not yet reassigned Canada M. Alfa (retired) and the original outbreak investigation team 0.02 Cluster XVIII: 4 species none reassigned 1015 Arlington St. Winnipeg MB Canada R3E 3R2 FOOTNOTES TO FIGURE I: 16S tree containing species assignable to the genus Clostridium sensu stricto ; all (ref 3); Shaun Tyler and staff of: NML’s DNA Core Facility, Dr. Phone: 1-204-789-2135 data from curated 16S rRNA sequences found in the NCBI database. Cluster XIX: 1 species not yet reassigned Garrett Westmacott of the NML’s Proteomic Core Facility, as EMAIL: kathy.bernard @ phac-aspc.gc.ca - BLACK species – validly named species in genus Clostridium . Taxa from genera Hathewaya, ‘Clostridioides’ and Atopobium serve as outgroups. We have elected to use sequence for C. felsineum as Other Clostridium spp: 18 species (not well as current (T. Burdz and D. Wiebe) and former staff of Twitter: @Trueperella shown here, rather than that described by Collins which fit cluster XI (ref 1). the Special Bacteriology unit (E. Ongsansoy, B. Ng, B. POSTER AND HANDOUT-AVAILABLE at: - SPECIES DEMARKED WITH *: omitted from the 2016 emendation of this genus by Lawson and Rainey (ref 2) assigned to a cluster) mostly reassigned to http: //umanitoba.ca/faculties/health_sciences /medicine /units - RED: ‘Clostridium neonatale (ref 5) fits this genus and will be proposed as a species novum Balcewich, T. Zimmerman) for technical assistance - ORANGE: 3 Eubacterium species will be reassigned to the genus Clostridium, based on this review other genera /medical_microbiology/faculty/KathrynBernard.html - PURPLE: Species have internet presence but are not validly named as of April 2017.