Multi-laboratory evaluation of the Illumina iSeq platform for whole genome sequencing of Salmonella, Escherichia coli and Listeria: This article is part of the Implementation of Genomics in Clinical and Public Health Microbiology collection&#160;

Patrick K. Mitchell; Leyi Wang; Bryce J. Stanhope; Brittany D. Cronk; Renee Anderson; Shipra Mohan; Lijuan Zhou; Susan Sanchez; Paula Bartlett; Carol Maddox; Vanessa DeShambo; Rinosh Mani; Lindsy M. Hengesbach; Sarah Gresch; Katie Wright; Sunil Mor; Shuping Zhang; Zhenyu Shen; Lifang Yan; Rebecca Mackey; Rebecca Franklin-Guild; Yan Zhang; Melanie Prarat; Katherine Shiplett; Akhilesh Ramachandran; Sai Narayanan; Justin Sanders; Andree A. Hunkapiller; Kevin Lahmers; Amanda A. Carbonello; Nicole Aulik; Ailam Lim; Jennifer Cooper; Angelica Jones; Jake Guag; Sarah M. Nemser; Gregory H. Tyson; Ruth Timme; Errol Strain; Renate Reimschuessel; Olgica Ceric; Laura B. Goodman

doi:10.1099/mgen.0.000717

Volume 8, Issue 2

Short Communication

Open Access

Multi-laboratory evaluation of the Illumina iSeq platform for whole genome sequencing of Salmonella, Escherichia coli and Listeria

This article is part of the Implementation of Genomics in Clinical and Public Health Microbiology collection

Patrick K. Mitchell¹, Leyi Wang², Bryce J. Stanhope¹, Brittany D. Cronk¹, Renee Anderson¹, Shipra Mohan³, Lijuan Zhou³, Susan Sanchez⁴, Paula Bartlett⁴, Carol Maddox², Vanessa DeShambo², Rinosh Mani⁵, Lindsy M. Hengesbach⁵, Sarah Gresch⁶, Katie Wright⁶, Sunil Mor⁶, Shuping Zhang⁷, Zhenyu Shen⁷, Lifang Yan⁸, Rebecca Mackey⁸, Rebecca Franklin-Guild¹, Yan Zhang⁹, Melanie Prarat⁹, Katherine Shiplett⁹, Akhilesh Ramachandran¹⁰, Sai Narayanan¹⁰, Justin Sanders¹¹, Andree A. Hunkapiller¹¹, Kevin Lahmers¹², Amanda A. Carbonello¹², Nicole Aulik¹³, Ailam Lim¹³, Jennifer Cooper¹³, Angelica Jones¹⁴, Jake Guag¹⁴, Sarah M. Nemser¹⁴, Gregory H. Tyson¹⁴, Ruth Timme¹⁵, Errol Strain¹⁴, Renate Reimschuessel¹⁴, Olgica Ceric¹⁴ and Laura B. Goodman¹
View Affiliations Hide Affiliations

Affiliations: ¹ Cornell University, College of Veterinary Medicine, Ithaca, NY, USA ² Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL, USA ³ Bronson Animal Disease Diagnostic Laboratory, Kissimmee, FL, USA ⁴ Athens Veterinary Diagnostic Laboratory, The University of Georgia, College of Veterinary Medicine,, GA, USA ⁵ Michigan State University, Veterinary Diagnostic Laboratory, Lansing, MI, USA ⁶ University of Minnesota, Veterinary Diagnostic Lboratory, Saint Paul, MN, USA ⁷ University of Missouri Veterinary Medical Diagnostic Laboratory, Columbia, MO, USA ⁸ Mississippi State University, Veterinary Diagnostic Laboratory, MS, USA ⁹ Ohio Department of Agriculture, Animal Disease Diagnostic Laboratory, Reynoldsburg, OH, USA ¹⁰ Oklahoma Animal Disease Diagnostic Laboratory, Oklahoma State University, Stillwater, OK, USA ¹¹ Oregon Veterinary Diagnostic Laboratory, Oregon State University, College of Veterinary Medicine, Corvallis, OR, USA ¹² Virginia-Maryland College of Veterinary Medicine, Blacksburg, VA, USA ¹³ University of Wisconsin-Madison Veterinary Diagnostic Laboratory, Madison, WI, USA ¹⁴ U.S. Food and Drug Administration, Center for Veterinary Medicine, Silver Spring, MD, USA ¹⁵ U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Silver Spring, MD, USA
*Correspondence: Leyi Wang, [email protected] *Correspondence: Laura B. Goodman, [email protected]
Published: 03 February 2022 https://doi.org/10.1099/mgen.0.000717

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.

Received: 02/06/2021
Accepted: 12/10/2021
Published Online: 03/02/2022

Keyword(s): foodborne illness , One Health , sequencing accessibility and sequencing quality

Funding

This study was supported by the:

u.s. food and drug administration (Award 1U18 FD006444-01)
- Principle Award Recipient: NotApplicable
u.s. food and drug administration (Award 5U18FD006160-02)
- Principle Award Recipient: NotApplicable
u.s. food and drug administration (Award 1U18FD006866-01)
- Principle Award Recipient: LeyiWang
u.s. food and drug administration (Award 1U18FD006714-01)
- Principle Award Recipient: LauraB. Goodman
u.s. food and drug administration (Award 1U18 FD006859-01)
- Principle Award Recipient: NotApplicable
u.s. food and drug administration (Award 1U18 FD006445-01)
- Principle Award Recipient: NotApplicable
u.s. food and drug administration (Award 1U18 FD006719-01)
- Principle Award Recipient: NotApplicable
u.s. food and drug administration (Award 1U18FD006671-01)
- Principle Award Recipient: NotApplicable
u.s. food and drug administration (Award 1U18 FD006555-01)
- Principle Award Recipient: NotApplicable
u.s. food and drug administration (Award 1U18 FD006714-01)
- Principle Award Recipient: NotApplicable
u.s. food and drug administration (Award 1U18 FD006866-01)
- Principle Award Recipient: NotApplicable
u.s. food and drug administration (Award 1U18 FD006460-01)
- Principle Award Recipient: NotApplicable
u.s. food and drug administration (Award 1U18 FD006568-01)
- Principle Award Recipient: NotApplicable
u.s. food and drug administration (Award 1U18 FD006593-01)
- Principle Award Recipient: NotApplicable

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

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Multi-laboratory evaluation of the Illumina iSeq platform for whole genome sequencing of Salmonella, Escherichia coli and Listeria

M Gen 8, 000717 (2022); https://doi.org/10.1099/mgen.0.000717

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Volume 8, Issue 2

Short Communication

Open Access

Multi-laboratory evaluation of the Illumina iSeq platform for whole genome sequencing of Salmonella, Escherichia coli and Listeria

This article is part of the Implementation of Genomics in Clinical and Public Health Microbiology collection

Abstract

Funding

Supplementary material 1

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