Here, we present the 3.53-Mb genome for Alcaligenaceae sp. strain 429, isolated from a patient with unknown etiology. While the 16S rRNA gene most closely resembles Paenalcaligenes species, average amino acid identity (AAI) analysis did not meet the threshold to classify our strain as a species of this family

Putonti, Catherine

Schreckenberger, Paul

Zilliox, Michael

English

Loyola eCommons

Loyola University Chicago Loyola eCommons Bioinformatics Faculty Publications Faculty Publications 2019 Draft Genome Sequence of Clinical Isolate Alcaligenaceae sp. Strain 429 Catherine Putonti Loyola University Chicago, cputonti@luc.edu Michael Zilliox Loyola University Chicago Paul Schreckenberger Loyola University Chicago Follow this and additional works at: https://ecommons.luc.edu/bioinformatics_facpub  Part of the Bioinformatics Commons Recommended Citation Putonti, Catherine; Zilliox, Michael; and Schreckenberger, Paul. Draft Genome Sequence of Clinical Isolate Alcaligenaceae sp. Strain 429. Microbiology Resource Announcements, , : , 2019. Retrieved from Loyola eCommons, Bioinformatics Faculty Publications, http://dx.doi.org/10.1128/MRA.00439-19 This Article is brought to you for free and open access by the Faculty Publications at Loyola eCommons. It has been accepted for inclusion in Bioinformatics Faculty Publications by an authorized administrator of Loyola eCommons. For more information, please contact ecommons@luc.edu. This work is licensed under a Creative Commons Attribution 4.0 License. Copyright © 2019 Zilliox et al. Draft Genome Sequence of Clinical Isolate Alcaligenaceae sp.Strain 429Michael J. Zilliox,a Paul C. Schreckenberger,b† Catherine Putontic,d,e,faDepartment of Public Health Sciences, Loyola University Chicago, Maywood, Illinois, USAbDepartment of Pathology, Loyola University Chicago, Maywood, Illinois, USAcDepartment of Computer Science, Loyola University Chicago, Chicago, Illinois, USAdBioinformatics Program, Loyola University Chicago, Chicago, Illinois, USAeDepartment of Biology, Loyola University Chicago, Chicago, Illinois, USAfDepartment of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, USAABSTRACT Here, we present the 3.53-Mb genome for Alcaligenaceae sp. strain 429,isolated from a patient with unknown etiology. While the 16S rRNA gene mostclosely resembles Paenalcaligenes species, average amino acid identity (AAI) analysisdid not meet the threshold to classify our strain as a species of this family.The bacterial isolate was received from Elmhurst Hospital in Elmhurst, IL, in 2012 foridentification. No patient data are available. Prior to sequencing, identification wasperformed using a matrix-assisted laser desorption ionization (MALDI) Biotyper (BrukerScientific, Billerica, MA, USA), which classified the strain as an Alcaligenes sp., whereasthe Vitek MS system (bioMérieux, Marcy-l’Étoile, France) found no match. However, 16SrRNA gene sequencing performed by our group indicated that the isolate was moreclosely related to another member of the Alcaligenaceae family, Paenalcaligenes su-wonensis. Paenalcaligenes species have been isolated from both the environment (1)and patients (2, 3), and only one genome has been sequenced for the genus to date (P.hominis). Furthermore, it is rarely associated with clinical symptoms (2, 3). In contrast,infections attributed to Alcaligenes faecalis have been reported, although they are rareand nosocomial (4–8). To resolve the taxonomy of this clinical isolate, we sequencedthe genome.The isolate was originally saved in Brucella broth with 10% glycerol and frozen at– 80°C. The frozen sample was then subcultured onto blood agar plates and incubatedat 35°C in 5% CO2 for 24 to 48 hours. Genomic DNA was extracted from bacterial cellsusing a validated mixture of lysozyme and mutanolysin and the DNeasy blood andtissue kit (Qiagen, Valencia, CA) (9). All steps were performed in a UV-irradiated,HEPA-filtered PCR workstation to minimize potential contaminants. The library wasconstructed using the Nextera XT kit (Illumina, San Diego, CA) following the manufac-turer’s protocol and sequenced on an Illumina MiSeq platform using a 500-cycle v2 kit(250  2 bp) rendering 1,336,945 paired-end reads.The raw reads first were trimmed using Sickle v1.33 (https://github.com/najoshi/sickle), specifying that trimmed reads of 30 nucleotides be removed from consider-ation (“-l 30”), and then assembled with SPAdes v3.11.1 using the “careful” option (10).Genome coverage was calculated for the contigs using the BBMap tool v37 (http://sourceforge.net/projects/bbmap/). Contigs with a length less than 600 bp or a coverageless than 60 (1 standard deviation from the mean coverage) were removed from furtherconsideration. The coverage was recalculated using BBMap as 98.64. The remaining391 contigs were queried via megablast against the nonredundant/nucleotide (nr/nt)database to confirm the genus and species of the isolate; all hits were to sequences ofCitation Zilliox MJ, Schreckenberger PC,Putonti C. 2019. Draft genome sequence ofclinical isolate Alcaligenaceae sp. strain 429.Microbiol Resour Announc 8:e00439-19.https://doi.org/10.1128/MRA.00439-19.Editor Frank J. Stewart, Georgia Institute ofTechnologyCopyright © 2019 Zilliox et al. This is an open-access article distributed under the terms ofthe Creative Commons Attribution 4.0International license.Address correspondence to Catherine Putonti,cputonti@luc.edu.† Deceased.Received 12 April 2019Accepted 22 April 2019Published 9 May 2019GENOME SEQUENCEScrossmVolume 8 Issue 19 e00439-19 mra.asm.org 1 on September 26, 2019 at LOYOLA UNIV CHICAGOhttp://mra.asm.org/Downloaded from strains belonging to the genera Paenalcaligenes and Alcaligenes. The contigs have atotal length of 3,539,013 nucleotides with a GC content of 50.1% and an N50 value of14,837 bp. The genome was annotated using the NCBI Prokaryotic Genome AnnotationPipeline (11). Three rRNA (1 5S, 1 16S, and 1 23S) gene sequences, 48 tRNA genesequences, and 3,422 protein coding genes were identified.The 16S rRNA sequence from the assembled genome was compared to NCBI’s 16SrRNA database via blastn, identifying the best hit to the P. suwonensis strain ABC02-12sequence (GenBank accession number NR_133804; query coverage, 93%; identity,99.16%). Average amino acid identity (AAI), calculated using the AAI-profiler onlineserver (12), identified the nearest neighbor as Alcaligenes faecalis (72%). The number ofcoding regions shared between our isolate and Paenalcaligenes and Alcaligenes strains,however, did not exceed 56%. This finding supports recent evidence suggesting thatthe Alcaligenes genus has an open pangenome (13). Thus, at this time, no genusdesignation can be made.Data availability. The draft whole-genome project for Alcaligenaceae sp. strain 429has been deposited at DDBJ/EMBL/GenBank under accession number SRSN00000000.Raw sequence reads are deposited at DDBJ/EMBL/GenBank under accession numberSRR8862657.ACKNOWLEDGMENTSWe acknowledge Kathleen McKinley for bacterial culture and isolation and GinaKuffel for whole-genome sequencing of the isolate.REFERENCES1. Moon J-Y, Lim J-M, Ahn J-H, Weon H-Y, Kwon S-W, Kim S-J. 2014.Paenalcaligenes suwonensis sp. nov., isolated from spent mushroomcompost. Int J Syst Evol Microbiol 64:882– 886. https://doi.org/10.1099/ijs.0.058412-0.2. Mukhopadhyay R, Joaquin J, Hogue R, Kilaru A, Jospin G, Mars K, EisenJA, Chaturvedi V. 2017. Complete genome sequence of a Paenalcaligeneshominis strain isolated from a paraplegic patient with neurogenic blad-der using single-molecule real-time sequencing technology. GenomeAnnounc 5:e00252-17. https://doi.org/10.1128/genomeA.00252-17.3. Kämpfer P, Falsen E, Langer S, Lodders N, Busse H-J. 2010. Paenalcali-genes hominis gen. nov., sp. nov., a new member of the family Alcali-genaceae. Int J Syst Evol Microbiol 60:1537–1542. https://doi.org/10.1099/ijs.0.016576-0.4. Bizet J, Bizet C. 1997. Strains of Alcaligenes faecalis from clinical material.J Infect 35:167–169. https://doi.org/10.1016/S0163-4453(97)91710-2.5. Ashwath ML, Katner HP. 2005. Pancreatic abscess secondary to Alcali-genes faecalis. Am J Med Sci 329:54 –55. https://doi.org/10.1097/00000441-200501000-00011.6. Pal SS, Panigrahi PK, Roy R, Nandi K, Das S. 2013. Endophthalmitis causedby Alcaligenes faecalis: a case series. Ocul Immunol Inflamm 21:446 – 448.https://doi.org/10.3109/09273948.2013.817592.7. Tena D, Fernández C, Lago MR. 2015. Alcaligenes faecalis: an unusualcause of skin and soft tissue infection. Jpn J Infect Dis 68:128 –130.https://doi.org/10.7883/yoken.JJID.2014.164.8. Chu AS, Harkness J. 2017. Alcaligenes faecalis cellulitis after a dog bite:case report and literature review. Pediatr Emerg Care 33:497– 498.https://doi.org/10.1097/PEC.0000000000000645.9. Yuan S, Cohen DB, Ravel J, Abdo Z, Forney LJ. 2012. Evaluation ofmethods for the extraction and purification of DNA from the humanmicrobiome. PLoS One 7:e33865. https://doi.org/10.1371/journal.pone.0033865.10. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS,Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV,Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a newgenome assembly algorithm and its applications to single-cell sequenc-ing. J Comput Biol 19:455– 477. https://doi.org/10.1089/cmb.2012.0021.11. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, ZaslavskyL, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J. 2016. NCBI ProkaryoticGenome Annotation Pipeline. Nucleic Acids Res 44:6614–6624. https://doi.org/10.1093/nar/gkw569.12. Medlar AJ, Törönen P, Holm L. 2018. AAI-profiler: fast proteome-wideexploratory analysis reveals taxonomic identity, misclassification andcontamination. Nucleic Acids Res 46:W479 –W485. https://doi.org/10.1093/nar/gky359.13. Basharat Z, Yasmin A, He T, Tong Y. 2018. Genome sequencing andanalysis of Alcaligenes faecalis subsp. phenolicus MB207. Sci Rep 8:3616.https://doi.org/10.1038/s41598-018-21919-4.Zilliox et al.Volume 8 Issue 19 e00439-19 mra.asm.org 2 on September 26, 2019 at LOYOLA UNIV CHICAGOhttp://mra.asm.org/Downloaded from 

Draft Genome Sequence of Clinical Isolate Alcaligenaceae sp. Strain 429

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Draft Genome Sequence of Clinical Isolate Alcaligenaceae sp. Strain 429

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