We report the first draft genome sequences of two isolates previously classified as CDC EF-4b species, Neisseria sp. 83E34 and Neisseria sp. 74A18. Both strains were isolated from patients with animal bites and likely constitute novel genomospecies with average nucleotide identities of &lt;95% to other sequenced strains

Chiu, Charles Y

Greninger, Alexander L

Miller, Steve

Streithorst, Jessica

English

PubMed

eScholarship - University of California

UCSFUC San Francisco Previously Published WorksTitleFirst Draft Genome Sequences of Neisseria sp. Strain 83E34 and Neisseria sp. Strain 74A18, Previously Identified as CDC Eugonic Fermenter 4b SpeciesPermalinkhttps://escholarship.org/uc/item/0xh5b6p1JournalMicrobiology Resource Announcements, 4(6)ISSN2576-098XAuthorsGreninger, Alexander LStreithorst, JessicaChiu, Charles Yet al.Publication Date2016-12-29DOI10.1128/genomea.01277-16 Peer reviewedeScholarship.org Powered by the California Digital LibraryUniversity of CaliforniaFirst Draft Genome Sequences of Neisseria sp. Strain 83E34 andNeisseria sp. Strain 74A18, Previously Identified as CDC EugonicFermenter 4b SpeciesAlexander L. Greninger, Jessica Streithorst, Charles Y. Chiu, Steve MillerDepartment of Laboratory Medicine, UCSF, San Francisco, California, USAWe report the first draft genome sequences of two isolates previously classified as CDC EF-4b species, Neisseria sp. 83E34 andNeisseria sp. 74A18. Both strains were isolated from patients with animal bites and likely constitute novel genomospecies withaverage nucleotide identities of <95% to other sequenced strains.Received 20 September 2016 Accepted 22 September 2016 Published 10 November 2016Citation Greninger AL, Streithorst J, Chiu CY, Miller S. 2016. First draft genome sequences of Neisseria sp. strain 83E34 and Neisseria sp. strain 74A18, previously identified asCDC eugonic fermenter 4b species. Genome Announc 4(6):e01277-16 doi:10.1128/genomeA.01277-16.Copyright © 2016 Greninger et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.Address correspondence to Steve Miller, steve.miller@ucsf.edu.CDC eugonic fermenter 4b (EF-4b) is a designation of Gram-negative bacteria that are members of animal oral flora andare typically isolated from animal bite wounds in humans (1). In2006, this group was identified as Neisseria zoodegmatis based on16S sequence and biochemical testing (1–3). Only five isolatesfrom human infections have been reported since the taxonomicalclassification of Neisseria zoodegmatis, while 30 isolates havebeen collected from CDC EF-4b bacteria (1, 4, 5). CDC EF-4b hasalso been cultured from a case of infectious tenosynovitis due to aSiberian tiger bite (6). To date, the 16S sequence is the only avail-able nucleotide sequence for Neisseria zoodegmatis.We sequenced the first draft genomes of two bacterial isolatesthat had been identified as CDC group EF-4b from the Universityof California, San Francisco (UCSF) microbiology lab. Isolate74A18 was isolated from a right-hand index finger culture of apatient with flexor tenosynovitis following a dog bite. Isolate83E34 was isolated from a left-lateral-hand culture of a patientwith cellulitis following a cate bite. Both patients also had Pasteu-rella multocida isolated concurrently from the wound cultures.DNA was extracted using the Qiagen EZ1 DNA tissue kit. Nex-tera XT paired-end and Nextera mate-pair libraries were se-quenced at 250/350 bp and 2  80 bp on an Illumina MiSeq,respectively, and on an Oxford Nanopore MinION sequencer.Illumina sequences were adapter and quality (Q20) trimmed us-ing cutadapt or NxTrim, de novo assembled using SPAdes version3.5, metagenomically screened for contaminating sequence withSURPI, and annotated via Prokka version 1.1 (7–12). A total of6,878,276 (74A18) and 9,380,478 (83E34) paired-end reads and4,052,930 (74A18) and 5,428,958 (83E34) mate-pair reads wererecovered after trimming. De novo assembly yielded 40 contigstotaling 2,419,010 bp, with an N50 of 233,412 bp for Neisseria sp.83E34, while Neisseria sp. 74A18 yielded 88 contigs totaling2,572,932 bp, with an N50 of 53,927 bp.BLASTN analysis of the 16S sequence from Neisseria sp. 74A18showed 98.6% identity to Neisseria shayeganii clone TM092 (ac-cession no. KM462144) and 98.1% identity to Neisseria zoodegma-tis strain N15a (accession no. JQ979306). BLASTN analysis of the16S sequence from Neisseria sp. 83E34 demonstrated 99.3% iden-tity to Neisseria canis oral taxon 137 (accession no. JN713302),98.2% identity to Neisseria shayeganii clone TM092 (accession no.KM462144), and 96.7% identity to Neisseria zoodegmatis strainN15a (accession no. JQ979306). However, alignment of Neisseriasp. 83E34 to Neisseria canis housekeeping genes revealed pooralignment (84.7% for rpoB [accession no. KM438030] and 88.4%for cpn60 [accession no. KJ872773]), suggesting it may not be astrain of Neisseria canis. Pairwise whole-genome alignment byLASTZ revealed 89.3% identity between our two sequenced spe-cies and 93.9% identity between Neisseria sp. 83E34 and Neisseriawadsworthii 9715 (WGS AGAZ01), the closest whole genomeavailable (13). These data are consistent with a high degree ofgenomic variability within related Neisseria spp. and isolates pre-viously identified as CDC EF-4 members (14). Further sequencingof EF-4b species, including Neisseria zoodegmatis, will be neededto fully classify these species.Accession number(s). These whole-genome shotgun proj-ects have been deposited at DDBJ/ENA/GenBank under theaccession numbers LGYH00000000 (Neisseria sp. 83E34) andLGZA00000000 (Neisseria sp. 74A18).ACKNOWLEDGMENTThis work was supported by the University of California, San Francisco,Department of Laboratory Medicine.REFERENCES1. Vandamme P, Holmes B, Bercovier H, Coenye T. 2006. Classification ofCenters for Disease Control Group eugonic fermenter (EF)-4a and EF-4bas Neisseria animaloris sp. nov. and Neisseria zoodegmatis sp. nov., respec-tively. Int J Syst Evol Microbiol 56:1801–1805. http://dx.doi.org/10.1099/ijs.0.64142-0.2. Rossau R, Vandenbussche G, Thielemans S, Segers P, Grosch H, GotheE, Mannheim W, De Ley J. 1989. Ribosomal ribonucleic acid cistronsimilarities and deoxyribonucleic acid homologies of Neisseria, Kingella,Eikenella, Simonsiella, Alysiella, and Centers for Disease Control groupsEF-4 and M-5 in the emended family Neisseriaceae. Int J Syst Bacteriol39:185–198. http://dx.doi.org/10.1099/00207713-39-2-185.3. Barrett SJ, Sneath PHA. 1994. A numerical phenotypic taxonomic studycrossmarkGenome AnnouncementsNovember/December 2016 Volume 4 Issue 6 e01277-16 genomea.asm.org 1of the genus Neisseria. Microbiology 140:2867–2891. http://dx.doi.org/10.1099/00221287-140-10-2867.4. Heydecke A, Andersson B, Holmdahl T, Melhus A. 2013. Humanwound infections caused by Neisseria animaloris and Neisseria zoodegma-tis, former CDC group EF-4a and EF-4b. Infect Ecol Epidemiol 3:20312.http://dx.doi.org/10.3402/iee.v3i0.20312.5. Ganière JP, Escande F, André-Fontaine G, Larrat M, Filloneau C. 1995.Characterization of group EF-4 bacteria from the oral cavity of dogs. VetMicrobiol 44:1–9. http://dx.doi.org/10.1016/0378-1135(94)00110-I.6. Isotalo PA, Edgar D, Toye B. 2000. Polymicrobial tenosynovitis withPasteurella multocida and other Gram negative bacilli after a Siberian tigerbite. J Clin Pathol 53:871– 872. http://dx.doi.org/10.1136/jcp.53.11.871.7. Seemann T. 2014. Prokka: rapid prokaryotic genome annotation. Bioin-formatics 30:2068 –2069. http://dx.doi.org/10.1093/bioinformatics/btu153.8. Naccache SN, Federman S, Veeraraghavan N, Zaharia M, Lee D, Sa-mayoa E, Bouquet J, Greninger AL, Luk K-C, Enge B, Wadford DA,Messenger SL, Genrich GL, Pellegrino K, Grard G, Leroy E, SchneiderBS, Fair JN, Martínez MA, Isa P, Crump JA, DeRisi JL, Sittler T,Hackett J, Miller S, Chiu CY. 2014. A cloud-compatible bioinformaticspipeline for ultrarapid pathogen identification from next-generation se-quencing of clinical samples. Genome Res 24:1180 –1192. http://dx.doi.org/10.1101/gr.171934.113.9. Martin M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J 17:10 –12. http://dx.doi.org/10.14806/ej.17.1.200.10. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, KulikovAS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV,Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012.SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455– 477. http://dx.doi.org/10.1089/cmb.2012.0021.11. Greninger AL, Langelier C, Cunningham G, Keh C, Melgar M, ChiuCY, Miller S. 2015. Two rapidly growing mycobacterial species isolatedfrom a brain abscess: first whole genome sequence of Mycobacterium im-munogenum and Mycobacterium llatzerense. J Clin Microbiol 53:2374 –2377. http://dx.doi.org/10.1128/JCM.00402-15.12. Greninger AL, Chorny I, Knowles S, Ng VL, Chaturvedi V. 2015. Draftgenome sequences of four NDM-1-producing Klebsiella pneumoniaestrains from a health care facility in northern California. Genome An-nounc 3(3):e00421-15. http://dx.doi.org/10.1128/genomeA.00421-15.13. Harris RS. 2007. Improved pairwise alignment of genomic DNA. Ph.D.thesis. Pennsylvania State University, Computer Science and Engineering,State College, PA.14. Roach DJ, Burton JN, Lee C, Stackhouse B, Butler-Wu SM, CooksonBT, Shendure J, Salipante SJ. 2015. A year of infection in the intensivecare unit: prospective whole genome sequencing of bacterial clinical iso-lates reveals cryptic transmissions and novel microbiota. PLoS Genet 11:e1005413. http://dx.doi.org/10.1371/journal.pgen.1005413.Greninger et al.Genome Announcements2 genomea.asm.org November/December 2016 Volume 4 Issue 6 e01277-16

First Draft Genome Sequences of Neisseria sp. Strain 83E34 and Neisseria sp. Strain 74A18, Previously Identified as CDC Eugonic Fermenter 4b Species

ABSTRACT
 
 We report the first draft genome sequences of two isolates previously classified as CDC EF-4b species,
 Neisseria
 sp. 83E34 and
 Neisseria
 sp. 74A18. Both strains were isolated from patients with animal bites and likely constitute novel genomospecies with average nucleotide identities of &lt;95% to other sequenced strains.
 </jats:p

Alexander L. Greninger

Jessica Streithorst

Charles Y. Chiu

Steve Miller

Crossref

Genome Announcements

First Draft Genome Sequences of
 Neisseria
 sp. Strain 83E34 and
 Neisseria
 sp. Strain 74A18
 ,
 Previously Identified as CDC Eugonic Fermenter 4b Species

https://escholarship.org/content/qt0xh5b6p1/qt0xh5b6p1.pdf?t=qafs2d

First Draft Genome Sequences of Neisseria sp. Strain 83E34 and Neisseria sp. Strain 74A18, Previously Identified as CDC Eugonic Fermenter 4b Species.

First Draft Genome Sequences of Neisseria sp. Strain 83E34 and Neisseria sp. Strain 74A18, Previously Identified as CDC Eugonic Fermenter 4b Species.

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