Evidence map›Paper›PMID 35113783›Full record

ArticleMicrobial genomics2022

Multi-laboratory evaluation of the Illumina iSeq platform for whole genome sequencing of

Patrick K Mitchell, Leyi Wang, Bryce J Stanhope, Brittany D Cronk, Renee Anderson, Shipra Mohan, Lijuan Zhou, Susan Sanchez, Paula Bartlett, Carol Maddox and 32 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Microbial genomics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.

0numbers the graph read from it
0cells of the map it votes in
8citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

8 citing papers in PubMed.

  1. Review
  2. Article
  3. No evidence of multidrug-resistantMicrobiology spectrum · 2025
    Observational
  4. Article
  5. Review
  6. Article
  7. Article
  8. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

42 authors.

Patrick K MitchellCornell University, College of Veterinary Medicine, Ithaca, NY, USA.
Leyi WangVeterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL, USA.
Bryce J StanhopeCornell University, College of Veterinary Medicine, Ithaca, NY, USA.
Brittany D CronkCornell University, College of Veterinary Medicine, Ithaca, NY, USA.
Renee AndersonCornell University, College of Veterinary Medicine, Ithaca, NY, USA.
Shipra MohanBronson Animal Disease Diagnostic Laboratory, Kissimmee, FL, USA.
Lijuan ZhouBronson Animal Disease Diagnostic Laboratory, Kissimmee, FL, USA.
Susan SanchezAthens Veterinary Diagnostic Laboratory, The University of Georgia, College of Veterinary Medicine,, GA, USA.
Paula BartlettAthens Veterinary Diagnostic Laboratory, The University of Georgia, College of Veterinary Medicine,, GA, USA.
Carol MaddoxVeterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL, USA.
Vanessa DeShamboVeterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL, USA.
Rinosh ManiMichigan State University, Veterinary Diagnostic Laboratory, Lansing, MI, USA.
Lindsy M HengesbachMichigan State University, Veterinary Diagnostic Laboratory, Lansing, MI, USA.
Sarah GreschUniversity of Minnesota, Veterinary Diagnostic Lboratory, Saint Paul, MN, USA.
Katie WrightUniversity of Minnesota, Veterinary Diagnostic Lboratory, Saint Paul, MN, USA.
Sunil MorUniversity of Minnesota, Veterinary Diagnostic Lboratory, Saint Paul, MN, USA.
Shuping ZhangUniversity of Missouri Veterinary Medical Diagnostic Laboratory, Columbia, MO, USA.
Zhenyu ShenUniversity of Missouri Veterinary Medical Diagnostic Laboratory, Columbia, MO, USA.
Lifang YanMississippi State University, Veterinary Diagnostic Laboratory, MS, USA.
Rebecca MackeyMississippi State University, Veterinary Diagnostic Laboratory, MS, USA.
Rebecca Franklin-GuildCornell University, College of Veterinary Medicine, Ithaca, NY, USA.
Yan ZhangOhio Department of Agriculture, Animal Disease Diagnostic Laboratory, Reynoldsburg, OH, USA.
Melanie PraratOhio Department of Agriculture, Animal Disease Diagnostic Laboratory, Reynoldsburg, OH, USA.
Katherine ShiplettOhio Department of Agriculture, Animal Disease Diagnostic Laboratory, Reynoldsburg, OH, USA.
Akhilesh RamachandranOklahoma Animal Disease Diagnostic Laboratory, Oklahoma State University, Stillwater, OK, USA.
Sai NarayananOklahoma Animal Disease Diagnostic Laboratory, Oklahoma State University, Stillwater, OK, USA.
Justin SandersOregon Veterinary Diagnostic Laboratory, Oregon State University, College of Veterinary Medicine, Corvallis, OR, USA.
Andree A HunkapillerOregon Veterinary Diagnostic Laboratory, Oregon State University, College of Veterinary Medicine, Corvallis, OR, USA.
Kevin LahmersVirginia-Maryland College of Veterinary Medicine, Blacksburg, VA, USA.
Amanda A CarbonelloVirginia-Maryland College of Veterinary Medicine, Blacksburg, VA, USA.
Nicole AulikUniversity of Wisconsin-Madison Veterinary Diagnostic Laboratory, Madison, WI, USA.
Ailam LimUniversity of Wisconsin-Madison Veterinary Diagnostic Laboratory, Madison, WI, USA.
Jennifer CooperUniversity of Wisconsin-Madison Veterinary Diagnostic Laboratory, Madison, WI, USA.
Angelica JonesU.S. Food and Drug Administration, Center for Veterinary Medicine, Silver Spring, MD, USA.
Jake GuagU.S. Food and Drug Administration, Center for Veterinary Medicine, Silver Spring, MD, USA.
Sarah M NemserU.S. Food and Drug Administration, Center for Veterinary Medicine, Silver Spring, MD, USA.
Gregory H TysonU.S. Food and Drug Administration, Center for Veterinary Medicine, Silver Spring, MD, USA.
Ruth TimmeU.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Silver Spring, MD, USA.
Errol StrainU.S. Food and Drug Administration, Center for Veterinary Medicine, Silver Spring, MD, USA.
Renate ReimschuesselU.S. Food and Drug Administration, Center for Veterinary Medicine, Silver Spring, MD, USA.
Olgica CericU.S. Food and Drug Administration, Center for Veterinary Medicine, Silver Spring, MD, USA.
Laura B GoodmanCornell University, College of Veterinary Medicine, Ithaca, NY, USA.

Funding

Genomic surveillance for antimicrobial resistance in animalsU18FD006716 · FDA · CORNELL UNIVERSITY · PI Laura Brunengraber Goodman · 2019 to 2026
$707k
Project Narrative - OADDL Testing Support for CVM Vet-LIRNU18FD006671 · FDA · OKLAHOMA STATE UNIVERSITY STILLWATER · PI Akhilesh Ramachandran · 2019 to 2026
$369k
Vet-LIRN Cooperative Agreement for Investigating Microbial, Chemical/Drug Contamination Events and Animal Feed-related OutbreaksU18FD006160 · FDA · FLORIDA STATE DEPT OF AGRIC/CONSUM SRVCS · PI Y. Reddy Bommineni · 2017 to 2026
$348k
Evaluation of the iSeq platform for E. coli pathotypingU18FD006714 · FDA · CORNELL UNIVERSITY · PI GOODMAN, LAURA BRUNENGRABER · 2019 to 2019
$225k
Improvement of sample processing, bioinformatic analysis and testing capacity for outbreak investigation of foodborne pathogens and antimicrobial resistance studies for FDA Vet-LIRNU18FD006555 · FDA · OHIO STATE DEPARTMENT OF AGRICULTURE · PI ZHANG, YAN · 2018 to 2018
$183k
FDA CV Vet-LRN Vet Diagnostic Lab ProgramU18FD006460 · FDA · UNIVERSITY OF MISSOURI-COLUMBIA · PI ZHANG, SHUPING · 2018 to 2018
$119k
Development of a harmonized method for sequencing Listeria monocytogenes on iSeqU18FD006866 · FDA · UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN · PI MADDOX, CAROL W., WANG, LEYI · 2019 to 2019
$97k
Expanding the capacity to sequence bacterial genomes and perform resistome analysis to most laboratories: bridging the gap between big sequencing centers and the diagnostic laboratoryU18FD006444 · FDA · UNIVERSITY OF GEORGIA · PI SANCHEZ, SUSAN · 2018 to 2018
$63k
Implementation of affordable whole genome sequencing for front-line genomic analysis of Escherchia coli of veterinary and human importanceU18FD006859 · FDA · UNIVERSITY OF WISCONSIN-MADISON · PI AULIK, NICOLE A · 2019 to 2019
$50k
Sequencing capacity in a veterinary diagnostic laboratoryU18FD006445 · FDA · VIRGINIA POLYTECHNIC INST AND ST UNIV · PI LAHMERS, KEVIN K · 2018 to 2018
$48k
Next Generation Sequencing for Oregon Veterinary Diagnostic LaboratoryU18FD006719 · FDA · OREGON STATE UNIVERSITY · PI ACKERMANN, MARK R · 2019 to 2019
$36k
Michigan State University VDL Vet-LIRN 2018U18FD006593 · FDA · MICHIGAN STATE UNIVERSITY · PI REAMS, RACHEL · 2018 to 2018
$31k
FDA HHS U18 FD006160FDA HHS U18 FD006444FDA HHS U18 FD006445FDA HHS U18 FD006460FDA HHS U18 FD006555FDA HHS U18 FD006568FDA HHS U18 FD006593FDA HHS U18 FD006671FDA HHS U18 FD006714FDA HHS U18 FD006716FDA HHS U18 FD006719FDA HHS U18 FD006859FDA HHS U18 FD006866
6 · The paper itself

Abstract

There is a growing need for public health and veterinary laboratories to perform whole genome sequencing (WGS) for monitoring antimicrobial resistance (AMR) and protecting the safety of people and animals. With the availability of smaller and more affordable sequencing platforms coupled with well-defined bioinformatic protocols, the technological capability to incorporate this technique for real-time surveillance and genomic epidemiology has greatly expanded. There is a need, however, to ensure that data are of high quality. The goal of this study was to assess the utility of a small benchtop sequencing platform using a multi-laboratory verification approach. Thirteen laboratories were provided the same equipment, reagents, protocols and bacterial reference strains. The Illumina DNA Prep and Nextera XT library preparation kits were compared, and 2×150 bp iSeq i100 chemistry was used for sequencing. Analyses comparing the sequences produced from this study with closed genomes from the provided strains were performed using open-source programs. A detailed, step-by-step protocol is publicly available via protocols.io (https://www.protocols.io/view/iseq-bacterial-wgs-protocol-bij8kcrw). The throughput for this method is approximately 4-6 bacterial isolates per sequencing run (20-26 Mb total load). The Illumina DNA Prep library preparation kit produced high-quality assemblies and nearly complete AMR gene annotations. The Prep method produced more consistent coverage compared to XT, and when coverage benchmarks were met, nearly all AMR, virulence and subtyping gene targets were correctly identified. Because it reduces the technical and financial barriers to generating WGS data, the iSeq platform is a viable option for small laboratories interested in genomic surveillance of microbial pathogens.

Indexed as

Genome, BacterialAnimalsBacteriaDNA, BacterialEscherichia coliEscherichia coli InfectionsFoodborne DiseasesGene LibraryGenomicsHigh-Throughput Nucleotide SequencingLaboratoriesListeriaSalmonellaSalmonella InfectionsVirulenceWhole Genome SequencingDNA, Bacterialfoodborne illnessOne Healthsequencing accessibilitysequencing quality

Identifiers

PMID35113783
PMCPMC8942033

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.