Metagenomic survey of antimicrobial resistance (AMR) in Maryland surface waters differentiated by high and low human impact

There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

ABSTRACT

Here, we examine surface waters as a modality to better understand baseline antimicrobial resistance (AMR) across the environment to supplement existing AMR monitoring in pathogens associated with humans, foods, and animals. Data from metagenomic and quasimetagenomic (shotgun sequenced enrichments) are used to describe AMR in Maryland surface waters from high and low human impact classifications.

Related collections

Most cited references 10

Record: found
Abstract: found
Article: found

Is Open Access

CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database

Brian P. Alcock, Amogelang Raphenya, Tammy Lau … (2019)

Abstract The Comprehensive Antibiotic Resistance Database (CARD; https://card.mcmaster.ca) is a curated resource providing reference DNA and protein sequences, detection models and bioinformatics tools on the molecular basis of bacterial antimicrobial resistance (AMR). CARD focuses on providing high-quality reference data and molecular sequences within a controlled vocabulary, the Antibiotic Resistance Ontology (ARO), designed by the CARD biocuration team to integrate with software development efforts for resistome analysis and prediction, such as CARD’s Resistance Gene Identifier (RGI) software. Since 2017, CARD has expanded through extensive curation of reference sequences, revision of the ontological structure, curation of over 500 new AMR detection models, development of a new classification paradigm and expansion of analytical tools. Most notably, a new Resistomes & Variants module provides analysis and statistical summary of in silico predicted resistance variants from 82 pathogens and over 100 000 genomes. By adding these resistance variants to CARD, we are able to summarize predicted resistance using the information included in CARD, identify trends in AMR mobility and determine previously undescribed and novel resistance variants. Here, we describe updates and recent expansions to CARD and its biocuration process, including new resources for community biocuration of AMR molecular reference data.

0 comments Cited 1023 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: found

Is Open Access

AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence

Michael Feldgarden, Vyacheslav V. Brover, Narjol Gonzalez-Escalona … (2021)

Antimicrobial resistance (AMR) is a significant public health threat. With the rise of affordable whole genome sequencing, in silico approaches to assessing AMR gene content can be used to detect known resistance mechanisms and potentially identify novel mechanisms. To enable accurate assessment of AMR gene content, as part of a multi-agency collaboration, NCBI developed a comprehensive AMR gene database, the Bacterial Antimicrobial Resistance Reference Gene Database and the AMR gene detection tool AMRFinder. Here, we describe the expansion of the Reference Gene Database, now called the Reference Gene Catalog, to include putative acid, biocide, metal, stress resistance genes, in addition to virulence genes and species-specific point mutations. Genes and point mutations are classified by broad functions, as well as more detailed functions. As we have expanded both the functional repertoire of identified genes and functionality, NCBI released a new version of AMRFinder, known as AMRFinderPlus. This new tool allows users the option to utilize only the core set of AMR elements, or include stress response and virulence genes, too. AMRFinderPlus can detect acquired genes and point mutations in both protein and nucleotide sequence. In addition, the evidence used to identify the gene has been expanded to include whether nucleotide or protein sequence was used, its location in the contig, and presence of an internal stop codon. These database improvements and functional expansions will enable increased precision in identifying AMR genes, linking AMR genotypes and phenotypes, and determining possible relationships between AMR, virulence, and stress response.

0 comments Cited 249 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: found

Is Open Access

MEGARes 2.0: a database for classification of antimicrobial drug, biocide and metal resistance determinants in metagenomic sequence data

Enrique Doster, Steven Lakin, Christopher J. Dean … (2019)

Abstract Antimicrobial resistance (AMR) is a threat to global public health and the identification of genetic determinants of AMR is a critical component to epidemiological investigations. High-throughput sequencing (HTS) provides opportunities for investigation of AMR across all microbial genomes in a sample (i.e. the metagenome). Previously, we presented MEGARes, a hand-curated AMR database and annotation structure developed to facilitate the analysis of AMR within metagenomic samples (i.e. the resistome). Along with MEGARes, we released AmrPlusPlus, a bioinformatics pipeline that interfaces with MEGARes to identify and quantify AMR gene accessions contained within a metagenomic sequence dataset. Here, we present MEGARes 2.0 (https://megares.meglab.org), which incorporates previously published resistance sequences for antimicrobial drugs, while also expanding to include published sequences for metal and biocide resistance determinants. In MEGARes 2.0, the nodes of the acyclic hierarchical ontology include four antimicrobial compound types, 57 classes, 220 mechanisms of resistance, and 1,345 gene groups that classify the 7,868 accessions. In addition, we present an updated version of AmrPlusPlus (AMR ++ version 2.0), which improves accuracy of classifications, as well as expanding scalability and usability.

0 comments Cited 124 times – based on 0 reviews      Review now

Bookmark

All references

Author and article information

Contributors

Brandon Kocurek:

ORCID: https://orcid.org/0000-0001-9313-2851

Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: Project administrationRole: Writing – original draftRole: Writing – review and editing

Shawn Behling: Role: ConceptualizationRole: Formal analysisRole: Methodology

Gordon Martin: Role: Data curationRole: Formal analysisRole: MethodologyRole: Project administration

Padmini Ramachandran:

ORCID: https://orcid.org/0000-0002-3958-3843

Role: Formal analysisRole: Methodology

Christopher Grim: Role: Data curation

Jie Zheng:

ORCID: https://orcid.org/0000-0003-3447-9681

Role: Methodology

Alison Franklin: Role: MethodologyRole: Project administration

Jay Garland: Role: ConceptualizationRole: Project administration

Daniel A. Tadesse: Role: Project administration

Manan Sharma:

ORCID: https://orcid.org/0000-0002-8585-0308

Role: MethodologyRole: Project administration

Gregory H. Tyson:

ORCID: https://orcid.org/0000-0002-2729-5035

Role: Project administrationRole: Writing – review and editing

Claudine Kabera: Role: Project administration

Heather Tate: Role: Project administrationRole: Writing – review and editing

Patrick F. McDermott:

ORCID: https://orcid.org/0000-0003-1868-8096

Role: ConceptualizationRole: Funding acquisitionRole: Project administrationRole: Writing – review and editing

Errol Strain: Role: ConceptualizationRole: Formal analysisRole: MethodologyRole: Writing – review and editing

Andrea Ottesen:

ORCID: https://orcid.org/0000-0002-6425-7943

Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: SupervisionRole: VisualizationRole: Writing – original draftRole: Writing – review and editing

Julia A. Maresca: Role: Editor

Journal

Journal ID (nlm-ta): Microbiol Resour Announc

Journal ID (iso-abbrev): Microbiol Resour Announc

Journal ID (publisher-id): mra

Title: Microbiology Resource Announcements

Publisher: American Society for Microbiology (1752 N St., N.W., Washington, DC )

ISSN (Electronic): 2576-098X

Publication date (Electronic, collection): January 2024

Publication date (Electronic, pub): 30 November 2023

Publication date PMC-release: 30 November 2023

Volume: 13

Issue: 1

Electronic Location Identifier: e00477-23

Affiliations

[1 ] Center for Veterinary Medicine, United States Food and Drug Administration; , Laurel, Maryland, USA

[2 ] Washington Department of Fish and Wildlife; , Seattle, Washington, USA

[3 ] Center for Food Safety and Applied Nutrition, United States Food and Drug Administration; , College Park, Maryland, USA

[4 ] Center for Environmental Measurement and Modeling, United States Environmental Protection Agency; , Cincinnati, Ohio, USA

[5 ] Environmental Microbial & Food Safety Lab, United States Department of Agriculture; , Beltsville, Maryland, USA

University of Delaware College of Engineering; , Newark, Delaware, USA

Author notes

Address correspondence to Andrea Ottesen, Andrea.Ottesen@ 123456fda.hhs.gov

Present address: Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, Maryland, USA

The authors declare no conflict of interest.

Author information

Brandon Kocurek https://orcid.org/0000-0001-9313-2851

Padmini Ramachandran https://orcid.org/0000-0002-3958-3843

Mark Mammel https://orcid.org/0000-0002-8273-6091

Jie Zheng https://orcid.org/0000-0003-3447-9681

Manan Sharma https://orcid.org/0000-0002-8585-0308

Gregory H. Tyson https://orcid.org/0000-0002-2729-5035

Patrick F. McDermott https://orcid.org/0000-0003-1868-8096

Andrea Ottesen https://orcid.org/0000-0002-6425-7943

Article

Publisher ID: 00477-23 Publisher ID: MRA.00477-23

DOI: 10.1128/MRA.00477-23

PMC ID: 10793305

PubMed ID: 38032210

SO-VID: 9e4feb30-f8ee-4cdc-862d-07163b5de256

License:

This is a work of the U.S. Government and is not subject to copyright protection in the United States. Foreign copyrights may apply.

History

Date received : 09 June 2023

Date accepted : 24 October 2023

Page count

supplementary-material: 0, authors: 18, Figures: 1, Tables: 1, References: 11, Pages: 4, Words: 1848

Funding

Funded by: National Antimicrobial Resistance Monitoring System (NARMS);

Award Recipient : Brandon Kocurek

Funded by: NARMS;

Award Recipient : Gordon Martin

Funded by: NARMS;

Award Recipient : Gregory H. Tyson

Funded by: NARMS;

Award Recipient : Patrick F. McDermott

Funded by: NARMS;

Award Recipient : Errol Strain

Funded by: NARMS;

Award Recipient : Andrea Ottesen

Custom metadata

cover-date January 2024

Keywords: surface water,antimicrobial resistance,narms,amr,metagenomic,quasimetagenomic,maryland,high human impact,low human impact,national antimicrobial resistance monitoring system

Data availability:

Keywords: surface water, antimicrobial resistance, narms, amr, metagenomic, quasimetagenomic, maryland, high human impact, low human impact, national antimicrobial resistance monitoring system

Metagenomic survey of antimicrobial resistance (AMR) in Maryland surface waters differentiated by high and low human impact

Read this article at

ABSTRACT

Related collections

Point-Of-Care Testing for AMR

Most cited references 10

CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database

AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence

MEGARes 2.0: a database for classification of antimicrobial drug, biocide and metal resistance determinants in metagenomic sequence data

Author and article information

Contributors

Journal

Affiliations

Author notes

Author information

Article

History

Page count

Funding

Categories

Custom metadata

Comments

Comment on this article

Similar content 106

Cited by 1

Most referenced authors 301