GENOME SEQUENCES
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Draft Genome Sequence of an Escherichia coli Strain
Harboring blaCTX-M-115, blaCMY-2, Aminoglycoside, Tetracycline,
and Sulfonamide Resistance Genes, Isolated from a Costa
Rican Wastewater Treatment Plant
Kenia Barrantes,a Luz María Chacón,a Eric Morales,a Lisbeth Ramírez-Carvajalb
aSección Infección-Nutrición, Instituto de Investigaciones en Salud (INISA), Universidad de Costa Rica, San José, Costa Rica
bLaboratorio Nacional de Servicios Veterinarios (LANASEVE), Servicio Nacional de Salud Animal (SENASA), Ministerio de Agricultura y Ganadería, Heredia, Costa Rica
ABSTRACT We report the draft genome sequence of the multidrug-resistant Esche-
richia coli strain PTA A1517-5, isolated from a wastewater treatment plant in Costa
Rica. The genome consists of 4,927,375 bp with a GC content of 50.57% and a total
of 4,853 genes. This strain harbors blaCTX-M-115, blaCMY-2, aminoglycoside, tetracy-
cline, and sulfonamide resistance genes.
Escherichia coli is a well-known and frequently used indicator of fecal pollution. Thisbacterium has also been shown to be a reservoir of antimicrobial resistance (AMR)
genes. Detection of E. coli harboring AMR genes could provide information on the
occurrence and spread of antibiotic resistance in the environment (1–5).
E. coli strain PTA A1517-5 was isolated from a wastewater sample which was
collected from the effluent of a domestic wastewater treatment plant (WWTP)
located in Alajuela, Costa Rica. E. coli organisms were enumerated from the WWTP
effluent using the most probable number (MPN) technique according to American
Public Health Association (APHA) guidelines (6). Briefly, the wastewater sample was
inoculated into lauryl tryptose broth (Oxoid) and incubated at 35.0°C for 48 h. All
tubes testing positive after the incubation period were inoculated into EC-MUG
broth (Oxoid). After a 24-h incubation period at 44.5°C, tubes with a positive
reaction were inoculated onto MacConkey agar plates (Oxoid) and incubated at
35°C for 24 h. The E. coli strain was identified using biochemical (API20E; BioMéri-
eux) and molecular (16S rRNA) methods (7).
Citation Barrantes K, Chacón LM, Morales E,
The antibiotic susceptibility profile was assessed according to 2014 CLSI guidelines (15). Ramírez-Carvajal L. 2020. Draft genome
The E. coli strain showed resistance to amoxicillin (AML), cephalothin (KF), cefazolin (KZ), sequence of an Escherichia coli strain harboring
cefotaxime (CTX), tetracycline (TE), gentamicin (CN), and trimethoprim-sulfamethoxazole blaCTX-M-115, blaCMY-2, aminoglycoside,
tetracycline, and sulfonamide resistance genes,
(SXT). isolated from a Costa Rican wastewater
After biochemical identification, a single colony of the E. coli strain was picked and treatment plant. Microbiol Resour Announc
further grown in Trypticase soy broth (Oxoid) at 35°C for 18 to 24 h. Genomic DNA was 9:e01015-19. https://doi.org/10.1128/MRA
.01015-19.
extracted from the E. coli strain using a DNeasy blood and tissue kit (Qiagen). DNA Editor David Rasko, University of Maryland
quality and quantity were measured using a NanoDrop instrument (Thermo Fisher, School of Medicine
Waltham, MA, USA) and a Quantus fluorometer (Promega, Wisconsin, USA). A dilution Copyright © 2020 Barrantes et al. This is an
of 0.2 ng/l of genomic DNA was used to prepare libraries with a Nextera XT DNA open-access article distributed under the terms
of the Creative Commons Attribution 4.0
library prep kit (Illumina, San Diego, CA, USA) following the manufacturer’s instructions. International license.
The library was sequenced on an Illumina MiSeq instrument using a paired-end (2  Address correspondence to Kenia Barrantes,
250-bp) protocol. kenia.barrantes@ucr.ac.cr.
The paired-end reads’ trimming quality was assessed using FastQC v0.11.5, and it Received 21 August 2019
Accepted 30 November 2019
was conducted with the seqtk toolkit (8) using the parameters q  0.1 and L  200. A Published 2 January 2020
total of 1,895,908 reads were obtained after trimming. Reads were assembled de novo
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Barrantes et al.
FIG 1 Genome alignment of E. coli strain PTA A1517-5 using the BLAST Ring Image Generator (BRIG) software (14). Multidrug efflux system genes
are denoted in brown letters (emrY, emrK, Bcr-1, mdtQ, mdtM, sugE, mdtK, norM, acrZ, mdfA/cmr, macA, macB, acrF, acrE, emrR, emrA, emrB, acrA,
acrB, mdtL, emrD, mdtA, mdtB, mdtC, mdtH, mdtG, marA, marC, marB, mdtE, and mdtF). Beta-lactamase genes (blaTEM, blaCTX-M-115, and blaCMY-2) are
denoted in blue letters. Class 1 integron genes (intI-1, dfrA12, gcuF, aadA2, qacEdelta1, and sul1) are marked with red letters. Aminoglycoside
resistance genes [ACC(3), APH(3)-I, APH(3), APH(6)-Ic, and APH(6)-Id] are denoted in purple letters, and tetracycline resistance genes [tet(B) and
tetR] are marked with green letters. The genome of E. coli strain ATCC 25922 was used as the reference (GenBank accession no. CP009072).
using SPAdes v3.13.0 (9) with default settings and included a built-in BayesHammer
read error correction tool. All contigs smaller than 500 bp were removed.
The genome was annotated using the NCBI Prokaryotic Genome Annotation Pipe-
line (PGAP) v4.8 (10).
The E. coli PTA A1517-5 draft genome sequence consists of 4,927,375 bp in 82
contigs with a GC content of 50.57%, an N50 value of 210,703 bp, a total of 4,853 genes,
and a genome coverage of 31.2.
AMR genes were queried in the ResFinder (11), PATRIC (12), and CARD databases
(13) using default parameters.
The antibiotic resistance phenotype of strain PTA A1517-5 was consistent with the
presence of blaCTX-M-115, blaCMY-2, aminoglycoside, tetracycline, and sulfonamide resis-
tance genes.
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Microbiology Resource Announcement
BLAST Ring Image Generator (BRIG) (14) was used to visualize the coding sequence
identity between the E. coli strain PTA A1517-5 and the reference E. coli strain ATCC
25922 (Fig. 1). Genes related to AMR are indicated in Fig. 1.
Data availability. This whole-genome shotgun sequencing project has been de-
posited in DDBJ/ENA/GenBank under the accession no. VMHG00000000. The version
described in this paper is version VMHG02000000. The reads were deposited in the
Sequence Read Archive (SRA) under accession no. PRJNA556251.
ACKNOWLEDGMENTS
This work was supported by Vicerrectoría de Investigación, Universidad de Costa
Rica and SENASA, Ministerio de Agricultura y Ganadería de Costa Rica.
Assembly and annotation of the E. coli strain PTA A1517-5 genome were partially
supported by a machine allocation on the Kabré supercomputer at the Centro Nacional
de Alta Tecnología (CeNAT).
We thank Erin Symonds for her valuable help in reading the manuscript.
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