ABSTRACT
 
 We sequenced a carbapenem-resistant
 Shewanella putrefaciens
 isolate cultured from the sink handle of a Pakistan hospital room. Assembly annotation indicates that the isolate has a chromosomal
 bla
 OXA-436
 carbapenemase and a plasmid-borne
 bla
 NDM-1
 gene. To our knowledge, this is the first report of a
 Shewanella
 species harboring
 bla
 NDM
 .
 </jats:p

Andleeb, Saadia

Burnham, Carey-Ann D

D-Souza, Alaric W

Dantas, Gautam

Gul, Danish

Kwon, Jennie H

Patel, Sanket

Potter, Robert F

Shupe, Angela

Wallace, Meghan A

English

Robert F. Potter

Alaric W. D’Souza

Meghan A. Wallace

Angela Shupe

Sanket Patel

Danish Gul

Jennie H. Kwon

Saadia Andleeb

Carey-Ann D. Burnham

Gautam Dantas

Crossref

Genome Announcements

Draft Genome Sequence of the
 bla
 OXA-436
 - and
 bla
 NDM-1
 -Harboring Shewanella putrefaciens SA70 Isolate

Digital Commons@Becker

Washington University School of MedicineDigital Commons@BeckerOpen Access Publications2017Draft genome sequence of the blaOXA-436- andblaNDM-1-harboring Shewanella putrefaciensSA70 isolateRobert F. PotterWashington University School of Medicine in St. LouisAlaric W. D-SouzaWashington University School of Medicine in St. LouisMeghan A. WallaceWashington University School of Medicine in St. LouisAngela ShupeWashington University School of Medicine in St. LouisSanket PatelWashington University School of Medicine in St. LouisSee next page for additional authorsFollow this and additional works at: https://digitalcommons.wustl.edu/open_access_pubsThis Open Access Publication is brought to you for free and open access by Digital Commons@Becker. It has been accepted for inclusion in OpenAccess Publications by an authorized administrator of Digital Commons@Becker. For more information, please contact engeszer@wustl.edu.Recommended CitationPotter, Robert F.; D-Souza, Alaric W.; Wallace, Meghan A.; Shupe, Angela; Patel, Sanket; Gul, Danish; Kwon, Jennie H.; Andleeb,Saadia; Burnham, Carey-Ann D.; and Dantas, Gautam, ,"Draft genome sequence of the blaOXA-436- and blaNDM-1-harboringShewanella putrefaciens SA70 isolate." Genome Announcements.5,29. e00644-17. (2017).https://digitalcommons.wustl.edu/open_access_pubs/6084AuthorsRobert F. Potter, Alaric W. D-Souza, Meghan A. Wallace, Angela Shupe, Sanket Patel, Danish Gul, Jennie H.Kwon, Saadia Andleeb, Carey-Ann D. Burnham, and Gautam DantasThis open access publication is available at Digital Commons@Becker: https://digitalcommons.wustl.edu/open_access_pubs/6084Draft Genome Sequence of theblaOXA-436- and blaNDM-1-HarboringShewanella putrefaciens SA70 IsolateRobert F. Potter,a Alaric W. D’Souza,a Meghan A. Wallace,b Angela Shupe,bSanket Patel,b Danish Gul,c Jennie H. Kwon,d Saadia Andleeb,cCarey-Ann D. Burnham,b,e,f Gautam Dantasa,b,f,gCenter for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis,Missouri, USAa; Department of Pathology and Immunology, Washington University School of Medicine, St.Louis, Missouri, USAb; Atta ur Rahman School of Applied Biosciences, National University of Sciences andTechnology Islamabad, Islamabad, Pakistanc; Division of Infectious Diseases, Washington University School ofMedicine, St. Louis, Missouri, USAd; Department of Pediatrics, St. Louis Children’s Hospital, St. Louis, Missouri,USAe; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri,USAf; Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USAgABSTRACT We sequenced a carbapenem-resistant Shewanella putrefaciens isolate cul-tured from the sink handle of a Pakistan hospital room. Assembly annotation indicatesthat the isolate has a chromosomal blaOXA-436 carbapenemase and a plasmid-borneblaNDM-1 gene. To our knowledge, this is the ﬁrst report of a Shewanella species harbor-ing blaNDM.Shewanella putrifaciens is an infrequent human pathogen associated with opportu-nistic infections (1–3). We isolated S. putrefaciens from the sink handle of anintensive care unit room from a tertiary care hospital in Pakistan using the Eswabcollection device and transport system (Becton, Dickinson, and Company). The isolatewas recovered on MacConkey agar with 5 g/mL cefotaxime (Hardy Diagnostics) andidentiﬁed with a conﬁdence value of 99.9% using VITEK matrix-assisted laser desorptionionization–time of ﬂight mass spectrometry (MALDI-TOF MS) with library version v2.3.3(bioMérieux, Durham, NC). Antimicrobial susceptibility testing using Kirby-Bauer diskdiffusion per Clinical and Laboratory Standards Institute M2 guidelines demonstratedan aztreonam zone size of 30 mm, ceftazidime zone size of 6 mm, meropenem zonesize of 6 mm, and imipenem zone size of 6 mm. Using Enterobacteriaceae, Pseudomonasaeruginosa, or Aeromonas sp. guidelines, the isolate is considered aztreonam suscep-tible but ceftazidime, meropenem, and imipenem resistant, a resistance proﬁle sug-gestive of a Class B carbapenemase. The isolate was also positive for phenotypicproduction of a carbapenemase via the carbapenem inactivation method (4). Toidentify known carbapenemase genes in S. putrefaciens, we extracted genomic DNAwith the Bacteremia kit (MoBIO, Carlsbad, CA), used 0.5 ng of DNA to make a NexteraXT Illumina sequencing library (5), and performed whole-genome sequencing on anIllumina NextSeq high-output sequencer to obtain 1,454,810 2  150 bp reads.We processed the sequence data on the High Throughput Computing Facility 2250processor computing cluster at Washington University, St. Louis School of Medicine.Nextera indexes and sequencing primers were trimmed from forward and reverse readsusing Trimmomatic, and human genome sequence reads, which may bleed throughfrom libraries on the same lane, were removed using DeconSeq (6, 7). The resulting1,452,994 paired-end reads were assembled with SPAdes (8). QUAST determined thatthe assembly contained 302 contigs (354,418 bp largest contig) and 70,827 bp N50 forcontigs with 0 nucleotides (9). We annotated contigs with lengths 500 bp, repre-senting 5,110,564 bp, using RAST (10). RAST identiﬁed 10 rRNA genes, 71 tRNA genes,Received 19 May 2017 Accepted 30 May2017 Published 20 July 2017Citation Potter RF, D’Souza AW, Wallace MA,Shupe A, Patel S, Gul D, Kwon JH, Andleeb S,Burnham C-AD, Dantas G. 2017. Draft genomesequence of the blaOXA-436- and blaNDM-1-harboring Shewanella putrefaciens SA70 isolate.Genome Announc 5:e00644-17. https://doi.org/10.1128/genomeA.00644-17.Copyright © 2017 Potter et al. This is an open-access article distributed under the terms ofthe Creative Commons Attribution 4.0International license.Address correspondence to Carey-Ann D.Burnham, cburnham@wustl.edu, or GautamDantas, dantas@wustl.edu.R.F.P. and A.W.D. contributed equally to thiswork.PROKARYOTEScrossmVolume 5 Issue 29 e00644-17 genomea.asm.org 1 on August 22, 2017 by Washington University in St. Louishttp://genomea.asm.org/Downloaded from and 4,522 CDS. Fifty percent of CDS have annotated functional systems. We identiﬁedantibiotic resistance genes with Resfams, ﬁnding two class D -lactamases and twoclass B -lactamases (11). BLASTp of the amino acid sequences against the NCBInonredundant protein database (accessed 14 March 2017) conﬁrmed these genes asblaOXA-436 (99% identity), blaOXA-10, a metallo-fold hydrolase, and blaNDM-1 (all 100%identity). OXA-436 (GenBank accession no. KT959103) and NDM-1 can hydrolyze car-bapenems, implicating them as the mechanism of carbapenem resistance (12). BLASTnof the blaNDM-1 contig against the nonredundant nucleotide database (accessed on 14March 2017) returned 100% identity to blaNDM-1 containing IncN type plasmids fromEscherichia coli (KJ440076) and Klebsiella pneumoniae (KJ440075) (13). The blaOXA-436carbapenemase contig had the highest BLASTn alignment score to the completegenome of Shewanella sp. MR-7 (CP000444).This Shewanella putrefaciens genome documents the diversity of host speciespossessing blaNDM-1. Identiﬁcation of carbapenemases in this isolate supports theimportance of antimicrobial susceptibility testing in infrequent pathogens. Importantly,Shewanella spp. could represent potential reservoirs for horizontally transferred anti-microbial resistance genes within the health care environment.Accession number(s). This whole-genome shotgun project has been deposited atDDBJ/ENA/GenBank under the accession no. NGZL00000000. The version described inthis paper is NGZL01000000.ACKNOWLEDGMENTSThis work was supported in part by a United States Agency for InternationalDevelopment award (3220-29047) to S.A., C.-A.D.B, and G.D. R.F.P. received supportfrom an NIGMS training grant through award T32 GM007067 (principal investigator,James Skeath). A.W.D. received support from an NIGMS training grant through awardT32 GM099538 (principal investigator, Wayne M. Yokoyama). J.H.K. received supportfrom the Washington University Institute of Clinical and Translational Sciences grantUL1TR000448, subaward KL2TR000450, from the National Center for Advancing Trans-lational Sciences of the National Institutes of Health.We thank Center for Genome Sciences & Systems Biology staff, Eric Martin, BrianKoebbe, and Jessica Hoisington-López for technical support and sequencing expertise.REFERENCES1. Janda JM, Abbott SL. 2014. The genus Shewanella: from the briny depthsbelow to human pathogen. Crit Rev Microbiol 40:293–312. https://doi.org/10.3109/1040841X.2012.726209.2. Wall JD, Krumholz LR. 2006. Uranium reduction. Annu Rev Microbiol60:149–166. https://doi.org/10.1146/annurev.micro.59.030804.121357.3. Tsai MS, You HL, Tang YF, Liu JW. 2008. Shewanella soft tissue infection:case report and literature review. Int J Infect Dis 12:e119–e124. https://doi.org/10.1016/j.ijid.2008.03.020.4. McMullen AR, Yarbrough ML, Wallace MA, Shupe A, Burnham CD. 2017.Evaluation of genotypic and phenotypic methods to detect carbapen-emase production in Gram-negative bacilli. Clin Chem 63:723–730.https://doi.org/10.1373/clinchem.2016.264804.5. Baym M, Kryazhimskiy S, Lieberman TD, Chung H, Desai MM, Kishony R.2015. Inexpensive multiplexed library preparation for megabase-sizedgenomes. PLoS One 10:e0128036. https://doi.org/10.1371/journal.pone.0128036.6. Schmieder R, Edwards R. 2011. Fast identiﬁcation and removal of se-quence contamination from genomic and metagenomic datasets. PLoSOne 6:e17288. https://doi.org/10.1371/journal.pone.0017288.7. Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a ﬂexible trimmer forIllumina sequence data. Bioinformatics 30:2114–2120. https://doi.org/10.1093/bioinformatics/btu170.8. 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.2012.0021.9. Gurevich A, Saveliev V, Vyahhi N, Tesler G. 2013. QUAST: quality assess-ment tool for genome assemblies. Bioinformatics 29:1072–1075. https://doi.org/10.1093/bioinformatics/btt086.10. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Edwards RA,Gerdes S, Parrello B, Shukla M, Vonstein V, Wattam AR, Xia F, Stevens R.2014. The SEED and the Rapid Annotation of microbial genomes usingSubsystems Technology (RAST). Nucleic Acids Res 42:D206–D214.https://doi.org/10.1093/nar/gkt1226.11. Gibson MK, Forsberg KJ, Dantas G. 2015. Improved annotation of anti-biotic resistance determinants reveals microbial resistomes cluster byecology. ISME J 9:207–216. https://doi.org/10.1038/ismej.2014.106.12. Yong D, Toleman MA, Giske CG, Cho HS, Sundman K, Lee K, Walsh TR.2009. Characterization of a new metallo-beta-lactamase gene, bla(NDM-1), and a novel erythromycin esterase gene carried on a unique geneticstructure in Klebsiella pneumoniae sequence type 14 from India. Antimi-crob Agents Chemother 53:5046–5054. https://doi.org/10.1128/AAC.00774-09.13. Chen CJ, Wu TL, Lu PL, Chen YT, Fung CP, Chuang YC, Lin JC, Siu LK.2014. Closely related NDM-1-encoding plasmids from Escherichia coliand Klebsiella pneumoniae in Taiwan. PLoS One 9:e104899. https://doi.org/10.1371/journal.pone.0104899.Potter et al.Volume 5 Issue 29 e00644-17 genomea.asm.org 2 on August 22, 2017 by Washington University in St. Louishttp://genomea.asm.org/Downloaded from 

Draft genome sequence of the blaOXA-436- and blaNDM-1-harboring Shewanella putrefaciens SA70 isolate

https://digitalcommons.wustl.edu/cgi/viewcontent.cgi?article=7087&amp;context=open_access_pubs

Draft genome sequence of the blaOXA-436- and blaNDM-1-harboring Shewanella putrefaciens SA70 isolate

Abstract

Similar works

Full text

Available Versions

Crossref

Digital Commons@Becker