Betancor, Laura

Chabalgoity, José Alejandro

Cordeiro, Nicolás F.

D'Alessandro, Bruno

Iriarte, Andrés

Pickard, Derek

Vignoli, Rafael

Yim, Lucía

English

LAReferencia - Red Federada de Repositorios Institucionales de Publicaciones Científicas Latinoamericanas

Draft Genome Sequences of Two Multidrug-ResistantSalmonella enterica Serovar Typhimurium Clinical Isolates fromUruguayNicolás F. Cordeiro,a Bruno D’Alessandro,b Andrés Iriarte,b Derek Pickard,c Lucía Yim,b José Alejandro Chabalgoity,bLaura Betancor,a Rafael VignoliaaDepartamento de Bacteriología y Virología, Instituto de Higiene, Facultad de Medicina, UDELAR, Montevideo,UruguaybDepartamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, UDELAR,Montevideo, UruguaycThe Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, United KingdomABSTRACT Multidrug-resistant Salmonella enterica isolates are an increasing prob-lem worldwide; nevertheless, the mechanisms responsible for such resistance arerarely well defined. Multidrug-resistant S. enterica serovar Typhimurium isolates ST3224and ST827 were collected from two patients. The characteristics of both genomes andantimicrobial resistance genes were determined using next-generation sequencing.Salmonella enterica is one of the main agents of foodborne diseases worldwide. Thismicroorganism is responsible for nearly 90 million cases of human gastroenteritisannually, representing losses that reach €3 billion in Europe and $3.2 billion in the UnitedStates (see http://www.efsa.europa.eu/en/topics/topic/salmonella.htm and http://www.ers.usda.gov/data-products/cost-estimates-of-foodborne-illnesses.aspx#48446). Althoughantimicrobial treatment is not indicated for uncomplicated infection, fluoroquinolones,oxyimino cephalosporins, and azithromycin constitute the first line of treatment forextraintestinal S. enterica infection. The extensive use of such antimicrobials has led tothe increase in antibiotic-resistant S. enterica isolates (1). We already reported theoccurrence in Uruguay of extended-spectrum -lactamases and plasmid-mediatedquinolone genes in S. enterica isolates, with blaCTX-M-14 and blaCTX-M-8 being the mostfrequently detected (2, 3).In the present study, two multidrug-resistant S. enterica serovar Typhimuriumclinical isolates, ST3324 and ST827, were sequenced to analyze the genetic traitsunderlying their resistance phenotypes. The two strains were obtained in 2012 fromfecal samples; ST3324 was isolated from an adult HIV patient, whereas ST827 wasrecovered from an elderly outpatient.Genomic DNA was extracted using the Qiagen DNeasy blood and tissue kit. Whole-genome sequencing was performed using the Illumina HiSeq 2000 platform in 50- to76-bp paired-end runs. High-quality reads were selected using Sickle (https://github.com/najoshi/sickle), and quality was assessed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). On average, 10,722,535 paired-end reads were pro-duced for each strain, resulting in more than 105-fold coverage of each genome. Denovo assembly was performed with SPAdes v. 3.6.1 (4) using a preassembly approachwith Velvet v. 1.2.10 (5). The assembly was created using a range of k-mer sizes between29 and 172 with a step of 2 and default parameters in both programs.Totals of 191 and 183 contigs were generated for strains ST3224 and ST827,respectively, with a GC content of approximately 52%. The genomes were annotatedusing the Rapid Annotations using Subsystem Technology (RAST) v. 2.0 server (6, 7);Received 27 June 2018 Accepted 6 July2018 Published 2 August 2018Citation Cordeiro NF, D’Alessandro B, Iriarte A,Pickard D, Yim L, Chabalgoity JA, Betancor L,Vignoli R. 2018. Draft genome sequences oftwo multidrug-resistant Salmonella entericaserovar Typhimurium clinical isolates fromUruguay. Microbiol Resour Announc 7:e00917-18. https://doi.org/10.1128/MRA.00917-18.Editor Frank J. Stewart, Georgia Institute ofTechnologyCopyright © 2018 Cordeiro et al. This is anopen-access article distributed under the termsof the Creative Commons Attribution 4.0International license.Address correspondence to Rafael Vignoli,rvignoli@higiene.edu.uy.L.B. and R.V. share senior authorship for thiswork.GENOME SEQUENCEScrossmVolume 7 Issue 4 e00917-18 mra.asm.org 1 on December 21, 2020 by guesthttp://mra.asm.org/Downloaded from strain ST3224 featured 5,020 coding sequences (CDS) and 102 RNA-coding genes,whereas strain ST827 presented 5,063 CDS and 113 RNA-coding genes. Multilocussequence typing (MLST) was conducted using MLST 2.0 (https://cge.cbs.dtu.dk/services/MLST/) (8), and both strains belonged to sequence type 19. Resistance genes werepredicted with ResFinder 3.0 (9), and results indicated that strain ST3224 harbored two-lactam resistance genes (blaCTX-M-14 and blaTEM-1), three aminoglycoside resistancegenes [aac(6=)-Iaa, aph(3=)-Ic, and aac(3)-IIa], one quinolone resistance gene (qnrB2),one macrolide resistance gene (ermB), one tetracycline resistance gene [tet(A)], andthree sulfonamide resistance genes (dfrA25 and two copies of sul1). On the other hand,strain ST827 featured -lactam resistance gene blaCTX-M-8, tetracycline resistance gene[tet(A)], sulfonamide resistance gene sul2, aminoglycoside resistance genes aac(6=)-Iaa,strA, and strB, and the phenicol resistance gene floR.The occurrence of Salmonella isolates featuring resistance genes to the currenttherapeutic options calls for active surveillance policies to reverse this phenomenon.Data availability. Sequence data of Uruguayan strains ST3224 and ST827 weredeposited at the European Nucleotide Archive under accession numbers ERS354131and ERS354132, respectively (BioSample numbers SAMEA2201728 and SAMEA2201729,respectively).ACKNOWLEDGMENTSWe thank The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Cam-pus, United Kingdom, and the Comisión Sectorial de Investigación Científica (CSIC),UDELAR.REFERENCES1. Wong MHY, Yan M, Chan EWC, Biao K, Chen S. 2014. Emergence of clinicalSalmonella enterica serovar Typhimurium isolates with concurrent resis-tance to ciprofloxacin, ceftriaxone, and azithromycin. Antimicrob AgentsChemother 58:3752–3756. https://doi.org/10.1128/AAC.02770-13.2. Cordeiro NF, Nabón A, García-Fulgueiras V, Álvez M, Sirok A, Camou T,Vignoli R. 2016. Analysis of plasmid mediated quinolone and oxyimino-cephalosporin resistance mechanisms in Uruguayan Salmonella entericaisolates from 2011–2013. J Glob Antimicrob Resist 6:165–171. https://doi.org/10.1016/j.jgar.2016.06.002.3. Bado I, Garcia-Fulgueiras V, Cordeiro NF, Betancor L, Caiata L, Seija V,Robino L, Algorta G, Chabalgoity JA, Ayala JA, Gutkind GO, Vignoli R.2012. First human isolate of Salmonella enterica serotype Enteritidisharboring blaCTX-M-14 in South America. Antimicrob Agents Chemother56:2132–2134. https://doi.org/10.1128/AAC.05530-11.4. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, LesinVM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N,Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a new genome as-sembly algorithm and its applications to single-cell sequencing. J ComputBiol 19:455– 477. https://doi.org/10.1089/cmb.2012.0021.5. Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short readassembly using de Bruijn graphs. Genome Res 18:821– 829. https://doi.org/10.1101/gr.074492.107.6. Aziz RK, Bartels D, Best A, DeJongh M, Disz T, Edwards RA, Formsma K,Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL,Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD,Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. 2008. TheRAST server: Rapid Annotations using Subsystems Technology. BMCGenomics 9:75. https://doi.org/10.1186/1471-2164-9-75.7. 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/gkt1226.8. Larsen MV, Cosentino S, Rasmussen S, Friis C, Hasman H, Marvig RL,Jelsbak L, Sicheritz-Ponten T, Ussery DW, Aarestrup FM, Lund O. 2012.Multilocus sequence typing of total-genome-sequenced bacteria. J ClinMicrobiol 50:1355–1361. https://doi.org/10.1128/JCM.06094-11.9. Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S, Lund O,Aarestrup FM, Larsen MV. 2012. Identification of acquired antimicrobialresistance genes. J Antimicrob Chemother 67:2640 –2644. https://doi.org/10.1093/jac/dks261.Cordeiro et al.Volume 7 Issue 4 e00917-18 mra.asm.org 2 on December 21, 2020 by guesthttp://mra.asm.org/Downloaded from 

Draft Genome Sequences of Two Multidrug-Resistant Salmonella enterica Serovar Typhimurium Clinical Isolates from Uruguay

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Draft Genome Sequences of Two Multidrug-Resistant Salmonella enterica Serovar Typhimurium Clinical Isolates from Uruguay

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