This article is a correction to:
Extended-Spectrum Beta-Lactamase Producing-Escherichia coli Isolated From Irrigation Waters and Produce in Ecuador
Lorena Montero
Jorge Irazabal2
Paul Cardenas
Jay P. Graham
Gabriel Trueba- 1Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
- 2Agrocalidad, Agencia de Regulación y Control Fito y Zoosanitario, Quito, Ecuador
- 3Environmental Health Sciences Division, University of California, Berkeley, Berkeley, CA, United States
A Corrigendum on
Extended-Spectrum Beta-Lactamase Producing-Escherichia coli Isolated From Irrigation Waters and Produce in Ecuador
by Montero, L., Irazabal, J., Cardenas, P., Graham, J. P., and Trueba, G. (2021). Front. Microbiol. 12:709418. doi: 10.3389/fmicb.2021.709418
In the original article, there was a mistake in the legend for Figure 3 as published. We included the word “host” by mistake. The correct legend appears below.
Figure 3. Phylogenetic tree of ESBL-E.coli sequences from irrigation water, fruits, and vegetables. Maximum likelihood phylogenetic tree of the core genomes of 80 ESBL-E.coli isolates from irrigation water, fruits, and vegetables. The labels show the isolate ID assigned according to the sample ID, the origin of the isolate is shown by source colors (irrigation water: blue, onion: brown, banana: yellow, blackberry: purple, strawberry: red, and garlic: green). The background colors highlighted on the branches of the tree indicate the seven identified phylogroups. Numbers represent bootstrap values using 1,000 pseudo-replicates.
In the original article, there was an error, the manuscript states that sequences were deposited in the European Nucleotide Archive but were deposited to Bioproject- NCBI.
A correction has been made to the Section Materials and Methods, “Sequence Accession Number,” paragraph one:
“The sequences were uploaded to Bioproject- NCBI under the following accession numbers: SAMN20872921, SAMN20872922, SAMN20872998, SAMN20873936, SAMN20873938, SAMN20873941, SAMN20873969, SAMN20873994, SAMN20874637, SAMN20875987, SAMN20875988, SAMN20875992, SAMN20875994, SAMN20875998, SAMN20879008, SAMN20879962, SAMN20879963, SAMN20879975, SAMN20879976, SAMN20880112, SAMN20880135, SAMN20880136, SAMN20881008, SAMN20881023, SAMN20881078, SAMN20881101, SAMN20881102, SAMN20881103, SAMN20881104, SAMN20881105, SAMN20881397, SAMN20881398, SAMN20881399, SAMN20881400, SAMN20882115, SAMN20882121, SAMN20882132, SAMN20882145, SAMN20882146, SAMN20882147, SAMN20882148, SAMN20882149, SAMN20883143, SAMN20883144, SAMN20883145, SAMN20883146, SAMN20883147, SAMN20884528, SAMN20884547, SAMN20884549, SAMN20886717, SAMN20887874, SAMN20887881, SAMN20887882, SAMN20887901, SAMN20887904, SAMN20887915, SAMN20887924, SAMN20887927, SAMN20887932, SAMN20887933, SAMN20888904, SAMN20888908, SAMN20888911, SAMN20888912, SAMN20888913, SAMN20888914, SAMN20888915, SAMN20888916, SAMN20888921, SAMN20888932, SAMN20888933, SAMN20888934, SAMN20888941, SAMN20888958, SAMN20888959, SAMN20888960, SAMN20888962, SAMN20890819, SAMN20891007.”
The original article contains texts identical to those found in another article published by our group.
A correction has been made to the Section Materials and Methods, “DNA Sequencing and Analysis:”
“Genomic DNA was extracted from the isolates using the Wizard® Genomic DNA Purification (Promega, United States) according to the manufacturer's instructions. Sequencing was carried out at the University of Minnesota Mid-Central Research and Outreach Center (Willmar, Minnesota) using a single 2 × 250-bp dual-index run on an Illumina MiSeq with Nextera XT libraries to generate ~30- to 50-fold coverage per genome. Genome assembly of MiSeq reads for each sample was performed using SPAdes assembler with the careful assembly option and automated k-mer detection (Bankevich et al., 2012). The identification of genus and species of the isolates was carried out using fastANI (Jain et al., 2018) with a percentage >80% of identification. Acquired AMR genes, plasmid types were identified using ABRicate tool (version 0.8.13), Resfinder was the database used for the identification of resistance genes (Zankari et al., 2012); PlasmidFinder database for plasmid replicon identification (Carattoli et al., 2014).”
A correction has been made to the Section Materials and Methods, “Phylogenetic Analysis,” paragraph one:
“Pan-genomic analysis was carried out with Roary (Page et al., 2015); the core genome of the isolates analyzed was defined with at least 99%. A maximum likelihood phylogenetic tree with (1,000 bootstrap replicates) was created based on the core genomes of the isolates using RaxML-NG (Kozlov et al., 2019). The phylogenetic tree was visualized using iTOL (Letunic and Bork, 2019). Additionally, multilocus sequence typing (MLST) (Larsen et al., 2012), based on seven housekeeping genes (adk, fumC, gyrB, icd, mdh, purA, and recA) and core genome (cgMLST) (Hansen et al., 2021) were performed using the Center for Genomic Epidemiology website1. The isolates also were characterized by Clermont phylogenetic typing by EzClermont web (Waters et al., 2020).”
The authors apologize for these errors that do not change the scientific conclusions of the article in any way. The original article has been updated.1
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Footnotes
References
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Keywords: fresh produce, irrigation water, ESBL E. coli, CTX-M, Extended-spectrum beta-lactamase (ESBL)
Citation: Montero L, Irazabal J, Cardenas P, Graham JP and Trueba G (2022) Corrigendum: Extended-Spectrum Beta-Lactamase Producing-Escherichia coli Isolated From Irrigation Waters and Produce in Ecuador. Front. Microbiol. 13:926514. doi: 10.3389/fmicb.2022.926514
Received: 22 April 2022; Accepted: 28 April 2022;
Published: 14 June 2022.
Approved by: Frontiers Editorial Office, Frontiers Media SA, Switzerland
Copyright © 2022 Montero, Irazabal, Cardenas, Graham and Trueba. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
*Correspondence: Gabriel Trueba, gtrueba@usfq.edu.ec