Antimicrobial resistance is a significant public health issue. We report here the draft genome sequences of three drug-resistant strains of commensal Escherichia coli isolated from a single healthy college student. Each strain has a distinct genome, but two of the three contain an identical large plasmid with multiple resistance genes

Garrett, Meghan

Parker, Jennifer

Stephens, Craig M.

English

PubMed

ABSTRACT
          
            Antimicrobial resistance is a significant public health issue. We report here the draft genome sequences of three drug-resistant strains of commensal
            Escherichia coli
            isolated from a single healthy college student. Each strain has a distinct genome, but two of the three contain an identical large plasmid with multiple resistance genes.
          </jats:p

Meghan Garrett

Jennifer Parker

Craig M. Stephens

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Genome Announcements

Draft Genome Sequences of Antibiotic-Resistant Commensal Escherichia coli

Scholar Commons - Santa Clara University

Santa Clara UniversityScholar CommonsBiology College of Arts & Sciences11-2014Draft Genome Sequences of Antibiotic-ResistantCommensal Escherichia coliMeghan GarrettJennifer ParkerCraig M. StephensSanta Clara University, cstephens@scu.eduFollow this and additional works at: http://scholarcommons.scu.edu/bioPart of the Genomics Commons, and the Microbiology CommonsCopyright © 2014 Garrett et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.This Article is brought to you for free and open access by the College of Arts & Sciences at Scholar Commons. It has been accepted for inclusion inBiology by an authorized administrator of Scholar Commons. For more information, please contact rscroggin@scu.edu.Recommended CitationGarrett M, Parker J, Stephens CM. 2014. Draft genome sequences of antibiotic-resistant commensal Escherichia coli. GenomeAnnounc. 2(6):e00873-14. doi:10.1128/ genomeA.00873-14.Draft Genome Sequences of Antibiotic-Resistant CommensalEscherichia coliMeghan Garrett, Jennifer Parker, Craig M. StephensBiology Department, Santa Clara University, Santa Clara, California, USAAntimicrobial resistance is a significant public health issue. We report here the draft genome sequences of three drug-resistantstrains of commensal Escherichia coli isolated from a single healthy college student. Each strain has a distinct genome, but two ofthe three contain an identical large plasmid with multiple resistance genes.Received 19 August 2014 Accepted 23 October 2014 Published 4 December 2014Citation Garrett M, Parker J, Stephens CM. 2014. Draft genome sequences of antibiotic-resistant commensal Escherichia coli. Genome Announc. 2(6):e00873-14. doi:10.1128/genomeA.00873-14.Copyright © 2014 Garrett et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.Address correspondence to Craig M. Stephens, cstephens@scu.edu.The antibiotic “resistome” within the normal human gut mi-crobiome is thought to contribute to the spread of resistancegenes to pathogens (1, 2). Escherichia coli readily moves betweenhumans, animals, and the environment (3, 4), and its ability topropagate mobile genetic elements may make it a significant vec-tor for the spread of resistance genes (5, 6). Here, we report thedraft genome sequences for three E. coli strains isolated from anundergraduate student, as part of a microbiology course project.The strains were isolated from rectal swabs plated on MacConkeyagar (Remel) with no antibiotic selection and then were screenedfor resistance to representatives of several classes of antibioticsusing a disk diffusion assay (Hardy Diagnostics). E. coli strainsCS02 and CS05, which were isolated months apart, are resistant toampicillin, erythromycin, gentamicin, streptomycin, sulfame-thoxazole, tetracycline, and trimethoprim. CS05 is additionallyresistant to nalidixic acid. E. coli strain CS03, which was isolatedfrom the same swab as CS02, is resistant to the -lactams ampi-cillin, cephalothin, and the combination of amoxicillin and clavu-lanic acid.Genomic DNA was isolated using the NucleoSpin tissue kit(Qiagen). Sequencing was performed on an Ion Torrent platform(Life Technologies) at the High-Throughput Genomics Center atthe University of Washington. The average read length was ~140bases. The read ends were trimmed in Geneious version 7.0.6(Biomatters Ltd.) before de novo assembly by MIRA (version 4.0)(7), initially using 45% of the reads to facilitate rapid assembly.Contigs500 bp were not included in the submission. Functionalannotation was performed by the NCBI Prokaryotic GenomesAutomatic Annotation Pipeline. The assembly metrics are pro-vided in Table 1.Resistance genes were identified in each strain by ResFinderversion 2.1 (8). Two of the strains (CS02 and CS05) contain con-tigs nearly identical to most of Klebsiella pneumoniae plasmidpKF3-140 (9). Sequences in common with pKF3-140 include a23-kb gene cluster encoding resistance to streptomycin-spectinomycin (aadA5), gentamicin [aac(3)-Iind], tetracycline(tetA), erythromycin (mphA), sulfonamides (folP alleles sul1 andsul2), and trimethoprim (dfrA17). -Lactam resistance attribut-able to blaTEM-1B is chromosomally encoded. Non-plasmid-derived contigs from strains CS02 and CS05 share only 96 to 98%identity, and only strain CS05 is resistant to nalidixic acid, due tocharacteristic mutations in gyrA. Strains CS02 and CS05 were iso-lated at different times, and the genome sequences suggest that theplasmid responsible for multidrug resistance moved horizontallybetween distinct E. coli lineages. Further analysis of these strainswill be presented in a future publication.Nucleotide sequence accession numbers. This whole-genome shotgun (WGS) project has been deposited atDDBJ/EMBL/GenBank under the WGS accession numbersJNOF00000000 (CS02), JNOG00000000 (CS03), andJNOI00000000 (CS05). The versions described here are the firstversions.TABLE 1 Accession numbers and assembly metrics for annotated E. coli draft whole-genome sequencesStrain NCBI accession no.No. of contigs500 bp N50No. of annotatedgenesNo. of predictedcoding sequencesCS02 JNOF00000000 278 69,714 5,020 4,392CS03 JNOG00000000 228 63,887 4,829 4,228CS05 JNOI00000000 245 58,975 4,872 4,397crossmarkGenome AnnouncementsNovember/December 2014 Volume 2 Issue 6 e00873-14 genomea.asm.org 1ACKNOWLEDGMENTWe acknowledge financial support for this project from Santa Clara Uni-versity.REFERENCES1. Sommer MO, Dantas G, Church GM. 2009. Functional characterizationof the antibiotic resistance reservoir in the human microflora. Science 325:1128 –1131. http://dx.doi.org/10.1126/science.1176950.2. Schjørring S, Krogfelt KA. 2011. Assessment of bacterial antibiotic resis-tance transfer in the gut. Int. J. Microbiol. 2011:312956. http://dx.doi.org/10.1155/2011/312956.3. Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M,Gill SR, Nelson KE, Relman DA. 2005. Diversity of the human intestinalmicrobial flora. Science 308:1635–1638. http://dx.doi.org/10.1126/ sci-ence.1110591.4. Radhouani H, Silva N, Poeta P, Torres C, Correia S, Igrejas G. 2014.Potential impact of antimicrobial resistance in wildlife, environment andhuman health. Front Microbiol. 5:23. http://dx.doi.org/10.3389/fmicb.2014.00023.5. Wright GD. 2007. The antibiotic resistome: the nexus of chemical andgenetic diversity. Nat. Rev. Microbiol. 5:175–186. http://dx.doi.org/10.1038/nrmicro1614.6. Bailey JK, Pinyon JL, Anantham S, Hall RM. 2010. Commensal Esche-richia coli of healthy humans: a reservoir for antibiotic-resistance determi-nants. J. Med. Microbiol. 59:1331–1339. http://dx.doi.org/10.1099/jmm.0.022475-0.7. Chevreux B. 2005. MIRA: an automated genome and EST assembler. Ph.D.thesis. German Cancer Research Center, Heidelberg, Heidelberg, Germany.8. Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S, LundO, Aarestrup FM, Larsen MV. 2012. Identification of acquired antimicro-bial resistance genes. J. Antimicrob. Chemother. 67:2640 –2644. http://dx.doi.org/10.1093/jac/dks261.9. Bai J, Liu Q, Yang Y, Wang J, Yang Y, Li J, Li P, Li X, Xi Y, Ying J, Ren P,Yang L, Ni L, Wu J, Bao Q, Zhou T. 2013. Insights into the evolution of geneorganization and multidrug resistance from Klebsiella pneumoniae plasmidpKF3-140. Gene 519:60–66. http://dx.doi.org/10.1016/j.gene.2013.01.050.Garrett et al.Genome Announcements2 genomea.asm.org November/December 2014 Volume 2 Issue 6 e00873-14

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Draft Genome Sequences of Antibiotic-Resistant Commensal Escherichia coli

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