Title: Escaping the fate of Sisyphus: assessing resistome hybridization baits for antimicrobial resistance gene capture

Abstract

Summary Finding, characterizing and monitoring reservoirs for antimicrobial resistance (AMR) is vital to protecting public health. Hybridization capture baits are an accurate, sensitive and cost‐effective technique used to enrich and characterize DNA sequences of interest, including antimicrobial resistance genes (ARGs), in complex environmental samples. We demonstrate the continued utility of a set of 19 933 hybridization capture baits designed from the Comprehensive Antibiotic Resistance Database (CARD)v1.1.2 and Pathogenicity Island Database (PAIDB)v2.0, targeting 3565 unique nucleotide sequences that confer resistance. We demonstrate the efficiency of our bait set on a custom‐made resistance mock community and complex environmental samples to increase the proportion of on‐target reads as much as >200‐fold. However, keeping pace with newly discovered ARGs poses a challenge when studying AMR, because novel ARGs are continually being identified and would not be included in bait sets designed prior to discovery. We provide imperative information on how our bait set performs against CARDv3.3.1, as well as a generalizable approach for deciding when and how to update hybridization capture bait sets. This research encapsulates the full life cycle of baits for hybridization capture of the resistome from design and validation (both in silico and in vitro ) to utilization and forecasting updates andmore » retirement.« less

Authors:

Beaudry, Megan S.  ^[1];

• Search DOE PAGES for author "Beaudry, Megan S."
• Search DOE PAGES for ORCID "0000-0002-5707-8648"

Thomas, Jesse C. ^[2]; Baptista, Rodrigo P.  ^[1];

• Search DOE PAGES for author "Baptista, Rodrigo P."
• Search DOE PAGES for ORCID "0000-0002-1806-8260"

Sullivan, Amanda H. ^[1]; Norfolk, William ^[1]; Devault, Alison ^[3]; Enk, Jacob ^[3]; Kieran, Troy J.  ^[1];

• Search DOE PAGES for author "Kieran, Troy J."
• Search DOE PAGES for ORCID "0000-0002-3711-0727"

Rhodes, Olin E. ^[4]; Perry‐Dow, K. Allison ^[5]; Rose, Laura J. ^[5]; Bayona‐Vásquez, Natalia J. ^[6]; Oladeinde, Adelumola ^[7]; Lipp, Erin K. ^[1]; Sanchez, Susan ^[1]; Glenn, Travis C. ^[1]

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+ Show Author Affiliations

1. University of Georgia, Athens, GA (United States)
2. University of Georgia, Athens, GA (United States); University of Georgia, Aiken, SC (United States). Savannah River Ecology Laboratory
3. Daicel Arbor Biosciences, Ann Arbor, MI (United States)
4. University of Georgia, Aiken, SC (United States). Savannah River Ecology Laboratory; University of Georgia, Athens, GA (United States)
5. Centers for Disease Control and Prevention (CDC), Atlanta, GA (United States)
6. University of Georgia, Athens, GA (United States); Emory University, Oxford, GA (United States)
7. US Department of Agriculture (USDA), Athens, GA (United States)

Publication Date:

Tue Sep 14 00:00:00 EDT 2021

Research Org.:

Univ. of Georgia, Athens, GA (United States)

Sponsoring Org.:

USDOE Office of Environmental Management (EM); US Department of Agriculture (USDA); Centers for Disease Control and Prevention (CDC)

OSTI Identifier:

1980609

Alternate Identifier(s):

OSTI ID: 1820680

Grant/Contract Number:  

FC09-07SR22506; 200-2018-2889; DE‐FC09‐07SR22506

Resource Type:

Accepted Manuscript

Journal Name:

Environmental Microbiology

Additional Journal Information:

Journal Volume: 23; Journal Issue: 12; Journal ID: ISSN 1462-2912

Publisher:

Wiley

Country of Publication:

United States

Language:

English

Subject:

59 BASIC BIOLOGICAL SCIENCES