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      Genomic epidemiology of extended-spectrum beta-lactamase-producing Escherichia coli from humans and a river in Aotearoa New Zealand

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          Abstract

          In Aotearoa New Zealand, urinary tract infections in humans are commonly caused by extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli. This group of antimicrobial-resistant bacteria are often multidrug resistant. However, there is limited information on ESBL-producing E. coli found in the environment and their link with human clinical isolates. In this study, we examined the genetic relationship between environmental and human clinical ESBL-producing E. coli and isolates collected in parallel within the same area over 14 months. Environmental samples were collected from treated effluent, stormwater and multiple locations along an Aotearoa New Zealand river. Treated effluent, stormwater and river water sourced downstream of the treated effluent outlet were the main samples that were positive for ESBL-producing E. coli (7/14 samples, 50.0%; 3/6 samples, 50%; and 15/28 samples, 54%, respectively). Whole-genome sequence comparison was carried out on 307 human clinical and 45 environmental ESBL-producing E. coli isolates. Sequence type 131 was dominant for both clinical (147/307, 47.9%) and environmental isolates (11/45, 24.4%). Only one ESBL gene was detected in each isolate. Among the clinical isolates, the most prevalent ESBL genes were bla CTX-M-27 (134/307, 43.6%) and bla CTX-M-15 (134/307, 43.6%). Among the environmental isolates, bla CTX-M-15 (28/45, 62.2%) was the most prevalent gene. A core SNP analysis of these isolates suggested that some strains were shared between humans and the local river. These results highlight the importance of understanding different transmission pathways for the spread of ESBL-producing E. coli.

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          Trimmomatic: a flexible trimmer for Illumina sequence data

          Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.
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            Prokka: rapid prokaryotic genome annotation.

            T Seemann (2014)
            The multiplex capability and high yield of current day DNA-sequencing instruments has made bacterial whole genome sequencing a routine affair. The subsequent de novo assembly of reads into contigs has been well addressed. The final step of annotating all relevant genomic features on those contigs can be achieved slowly using existing web- and email-based systems, but these are not applicable for sensitive data or integrating into computational pipelines. Here we introduce Prokka, a command line software tool to fully annotate a draft bacterial genome in about 10 min on a typical desktop computer. It produces standards-compliant output files for further analysis or viewing in genome browsers. Prokka is implemented in Perl and is freely available under an open source GPLv2 license from http://vicbioinformatics.com/. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
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              CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

              Large-scale recovery of genomes from isolates, single cells, and metagenomic data has been made possible by advances in computational methods and substantial reductions in sequencing costs. Although this increasing breadth of draft genomes is providing key information regarding the evolutionary and functional diversity of microbial life, it has become impractical to finish all available reference genomes. Making robust biological inferences from draft genomes requires accurate estimates of their completeness and contamination. Current methods for assessing genome quality are ad hoc and generally make use of a limited number of “marker” genes conserved across all bacterial or archaeal genomes. Here we introduce CheckM, an automated method for assessing the quality of a genome using a broader set of marker genes specific to the position of a genome within a reference genome tree and information about the collocation of these genes. We demonstrate the effectiveness of CheckM using synthetic data and a wide range of isolate-, single-cell-, and metagenome-derived genomes. CheckM is shown to provide accurate estimates of genome completeness and contamination and to outperform existing approaches. Using CheckM, we identify a diverse range of errors currently impacting publicly available isolate genomes and demonstrate that genomes obtained from single cells and metagenomic data vary substantially in quality. In order to facilitate the use of draft genomes, we propose an objective measure of genome quality that can be used to select genomes suitable for specific gene- and genome-centric analyses of microbial communities.
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                Author and article information

                Contributors
                Journal
                Microb Genom
                Microb Genom
                mgen
                mgen
                Microbial Genomics
                Microbiology Society
                2057-5858
                2025
                10 January 2025
                10 January 2025
                : 11
                : 1
                : 001341
                Affiliations
                [1 ]departmentmEpiLab, School of Veterinary Science , Massey University , Palmerston North, New Zealand
                [2 ]departmentSchool of Food Technology and Natural Sciences , Massey University , Palmerston North, New Zealand
                [3 ]departmentNew Zealand Food Safety Science and Research Centre , Massey University , Palmerston North, New Zealand
                Author notes

                The authors declare that there are no conflicts of interest.

                Supplementary material: Two supplementary figures and one supplementary tables are available with the online version of this article.

                Author information
                http://orcid.org/0000-0001-5906-2941
                http://orcid.org/0000-0002-0285-4101
                http://orcid.org/0000-0001-5731-3233
                http://orcid.org/0000-0001-7585-7795
                http://orcid.org/0000-0001-8879-4535
                http://orcid.org/0000-0003-1449-7321
                Article
                001341
                10.1099/mgen.0.001341
                11718517
                39791259
                4cb3c226-3a16-43c2-9e82-9031c27c0e59
                Copyright © 2025 The authors

                This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.

                History
                : 08 May 2024
                : 03 December 2024
                Funding
                Funded by: Hawkes Bay Research Medical Foundation
                Award ID: N/A
                Award Recipient :
                Funded by: http://dx.doi.org/10.13039/100012500; Palmerston North Medical Research Foundation
                Award ID: N/A
                Award Recipient :
                Categories
                Research Article
                Pathogens and Epidemiology

                antimicrobial resistance,e. coli,esbl,freshwater,urinary tract infection

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