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

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 C 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

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

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 C Gresch, Katie Wright, Sunil Mor, Shuping Zhang, Zhenyu Shen, Lifang Yan, Rebecca MackeyRebecca 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

Research output: Contribution to journal › Article › peer-review

6 Scopus citations

Abstract

There is a growing need for public health and veterinary laboratories to perform whole genome sequencing (WGS) for monitor-ing 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 cor-rectly 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.

Original language	English (US)
Article number	000717
Journal	Microbial genomics
Volume	8
Issue number	2
DOIs	https://doi.org/10.1099/mgen.0.000717
State	Published - 2022

Bibliographical note

Funding Information:
This study was funded (PAR-18-604) and performed in collaboration with the Food and Drug Administration?s Veterinary Laboratory Investigation and Response Network (FDA Vet-LIRN) under cooperative agreements 1U18FD006714-01 to L.B.G. and 1U18FD006866-01 to L.W. Additional funding for participating laboratories was as follows: 5U18FD006160-02, Florida Department of Agriculture and Consumer Services; 1U18 FD006444-01, Athens Veterinary Diagnostic Laboratory, The University of Georgia; 1U18 FD006593-01, Michigan State University, Veterinary Diagnostic Labora-tory; 1U18 FD006568-01, University of Minnesota, Veterinary Diagnostic Laboratory; 1U18 FD006460-01, University of Missouri, Veterinary Medical Diagnostic Laboratory; 1U18 FD006866-01, 1U18 FD006714-01, Mississippi State University, Veterinary Diagnostic Laboratory; 1U18 FD006555-01, Ohio Animal Disease Diagnostic Laboratory; 1U18FD006671-01, Oklahoma Animal Disease Diagnostic Laboratory, Oklahoma State University; 1U18 FD006719-01, Oregon Veterinary Diagnostic Laboratory, Oregon State University; 1U18 FD006445-01, Virginia-Maryland College of Veterinary Medicine; 1U18 FD006859-01, University of Wisconsin-Madison Veterinary Diagnostic Laboratory.

Funding Information:
This study was funded (PAR-18-604) and performed in collaboration with the Food and Drug Administration’s Veterinary Laboratory Investigation and Response Network (FDA Vet-LIRN) under cooperative agreements 1U18FD006714-01 to L.B.G. and 1U18FD006866-01 to L.W. Additional funding for participating laboratories was as follows: 5U18FD006160-02, Florida Department of Agriculture and Consumer Services; 1U18 FD006444-01, Athens Veterinary Diagnostic Laboratory, The University of Georgia; 1U18 FD006593-01, Michigan State University, Veterinary Diagnostic Laboratory; 1U18 FD006568-01, University of Minnesota, Veterinary Diagnostic Laboratory; 1U18 FD006460-01, University of Missouri, Veterinary Medical Diagnostic Laboratory; 1U18 FD006866-01, 1U18 FD006714-01, Mississippi State University, Veterinary Diagnostic Laboratory; 1U18 FD006555-01, Ohio Animal Disease Diagnostic Laboratory; 1U18FD006671-01, Oklahoma Animal Disease Diagnostic Laboratory, Oklahoma State University; 1U18 FD006719-01, Oregon Veterinary Diagnostic Laboratory, Oregon State University; 1U18 FD006445-01, Virginia-Maryland College of Veterinary Medicine; 1U18 FD006859-01, University of Wisconsin-Madison Veterinary Diagnostic Laboratory.

Publisher Copyright:
© 2022, Microbiology Society. All rights reserved.

Keywords

One Health
foodborne illness
sequencing accessibility
sequencing quality

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Publisher link

10.1099/mgen.0.000717

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Mitchell, P. K., Wang, L., Stanhope, B. J., Cronk, B. D., Anderson, R., Mohan, S., Zhou, L., Sanchez, S., Bartlett, P., Maddox, C., Deshambo, V., Mani, R., Hengesbach, L. M., Gresch, S. C., Wright, K., Mor, S., Zhang, S., Shen, Z., Yan, L., ... Goodman, L. B. (2022). Multi-laboratory evaluation of the Illumina iSeq platform for whole genome sequencing of Salmonella, Escherichia coli and Listeria. Microbial genomics, 8(2), Article 000717. https://doi.org/10.1099/mgen.0.000717

Mitchell, PK, Wang, L, Stanhope, BJ, Cronk, BD, Anderson, R, Mohan, S, Zhou, L, Sanchez, S, Bartlett, P, Maddox, C, Deshambo, V, Mani, R, Hengesbach, LM, Gresch, SC, Wright, K, Mor, S, Zhang, S, Shen, Z, Yan, L, Mackey, R, Franklin-Guild, R, Zhang, Y, Prarat, M, Shiplett, K, Ramachandran, A, Narayanan, S, Sanders, J, Hunkapiller, AA, Lahmers, K, Carbonello, AA, Aulik, N, Lim, A, Cooper, J, Jones, A, Guag, J, Nemser, SM, Tyson, GH, Timme, R, Strain, E, Reimschuessel, R, Ceric, O & Goodman, LB 2022, 'Multi-laboratory evaluation of the Illumina iSeq platform for whole genome sequencing of Salmonella, Escherichia coli and Listeria', Microbial genomics, vol. 8, no. 2, 000717. https://doi.org/10.1099/mgen.0.000717

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

abstract = "There is a growing need for public health and veterinary laboratories to perform whole genome sequencing (WGS) for monitor-ing 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 cor-rectly 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.",

keywords = "One Health, foodborne illness, sequencing accessibility, sequencing quality",

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

note = "Funding Information: This study was funded (PAR-18-604) and performed in collaboration with the Food and Drug Administration?s Veterinary Laboratory Investigation and Response Network (FDA Vet-LIRN) under cooperative agreements 1U18FD006714-01 to L.B.G. and 1U18FD006866-01 to L.W. Additional funding for participating laboratories was as follows: 5U18FD006160-02, Florida Department of Agriculture and Consumer Services; 1U18 FD006444-01, Athens Veterinary Diagnostic Laboratory, The University of Georgia; 1U18 FD006593-01, Michigan State University, Veterinary Diagnostic Labora-tory; 1U18 FD006568-01, University of Minnesota, Veterinary Diagnostic Laboratory; 1U18 FD006460-01, University of Missouri, Veterinary Medical Diagnostic Laboratory; 1U18 FD006866-01, 1U18 FD006714-01, Mississippi State University, Veterinary Diagnostic Laboratory; 1U18 FD006555-01, Ohio Animal Disease Diagnostic Laboratory; 1U18FD006671-01, Oklahoma Animal Disease Diagnostic Laboratory, Oklahoma State University; 1U18 FD006719-01, Oregon Veterinary Diagnostic Laboratory, Oregon State University; 1U18 FD006445-01, Virginia-Maryland College of Veterinary Medicine; 1U18 FD006859-01, University of Wisconsin-Madison Veterinary Diagnostic Laboratory. Funding Information: This study was funded (PAR-18-604) and performed in collaboration with the Food and Drug Administration{\textquoteright}s Veterinary Laboratory Investigation and Response Network (FDA Vet-LIRN) under cooperative agreements 1U18FD006714-01 to L.B.G. and 1U18FD006866-01 to L.W. Additional funding for participating laboratories was as follows: 5U18FD006160-02, Florida Department of Agriculture and Consumer Services; 1U18 FD006444-01, Athens Veterinary Diagnostic Laboratory, The University of Georgia; 1U18 FD006593-01, Michigan State University, Veterinary Diagnostic Laboratory; 1U18 FD006568-01, University of Minnesota, Veterinary Diagnostic Laboratory; 1U18 FD006460-01, University of Missouri, Veterinary Medical Diagnostic Laboratory; 1U18 FD006866-01, 1U18 FD006714-01, Mississippi State University, Veterinary Diagnostic Laboratory; 1U18 FD006555-01, Ohio Animal Disease Diagnostic Laboratory; 1U18FD006671-01, Oklahoma Animal Disease Diagnostic Laboratory, Oklahoma State University; 1U18 FD006719-01, Oregon Veterinary Diagnostic Laboratory, Oregon State University; 1U18 FD006445-01, Virginia-Maryland College of Veterinary Medicine; 1U18 FD006859-01, University of Wisconsin-Madison Veterinary Diagnostic Laboratory. Publisher Copyright: {\textcopyright} 2022, Microbiology Society. All rights reserved.",

year = "2022",

doi = "10.1099/mgen.0.000717",

language = "English (US)",

volume = "8",

journal = "Microbial genomics",

issn = "2057-5858",

publisher = "Microbiology Society",

number = "2",

}

TY - JOUR

T1 - Multi-laboratory evaluation of the Illumina iSeq platform for whole genome sequencing of Salmonella, Escherichia coli and Listeria

AU - Mitchell, Patrick K.

AU - Wang, Leyi

AU - Stanhope, Bryce J.

AU - Cronk, Brittany D.

AU - Anderson, Renee

AU - Mohan, Shipra

AU - Zhou, Lijuan

AU - Sanchez, Susan

AU - Bartlett, Paula

AU - Maddox, Carol

AU - Deshambo, Vanessa

AU - Mani, Rinosh

AU - Hengesbach, Lindsy M.

AU - Gresch, Sarah C

AU - Wright, Katie

AU - Mor, Sunil

AU - Zhang, Shuping

AU - Shen, Zhenyu

AU - Yan, Lifang

AU - Mackey, Rebecca

AU - Franklin-Guild, Rebecca

AU - Zhang, Yan

AU - Prarat, Melanie

AU - Shiplett, Katherine

AU - Ramachandran, Akhilesh

AU - Narayanan, Sai

AU - Sanders, Justin

AU - Hunkapiller, Andree A.

AU - Lahmers, Kevin

AU - Carbonello, Amanda A.

AU - Aulik, Nicole

AU - Lim, Ailam

AU - Cooper, Jennifer

AU - Jones, Angelica

AU - Guag, Jake

AU - Nemser, Sarah M.

AU - Tyson, Gregory H.

AU - Timme, Ruth

AU - Strain, Errol

AU - Reimschuessel, Renate

AU - Ceric, Olgica

AU - Goodman, Laura B.

N1 - Funding Information: This study was funded (PAR-18-604) and performed in collaboration with the Food and Drug Administration?s Veterinary Laboratory Investigation and Response Network (FDA Vet-LIRN) under cooperative agreements 1U18FD006714-01 to L.B.G. and 1U18FD006866-01 to L.W. Additional funding for participating laboratories was as follows: 5U18FD006160-02, Florida Department of Agriculture and Consumer Services; 1U18 FD006444-01, Athens Veterinary Diagnostic Laboratory, The University of Georgia; 1U18 FD006593-01, Michigan State University, Veterinary Diagnostic Labora-tory; 1U18 FD006568-01, University of Minnesota, Veterinary Diagnostic Laboratory; 1U18 FD006460-01, University of Missouri, Veterinary Medical Diagnostic Laboratory; 1U18 FD006866-01, 1U18 FD006714-01, Mississippi State University, Veterinary Diagnostic Laboratory; 1U18 FD006555-01, Ohio Animal Disease Diagnostic Laboratory; 1U18FD006671-01, Oklahoma Animal Disease Diagnostic Laboratory, Oklahoma State University; 1U18 FD006719-01, Oregon Veterinary Diagnostic Laboratory, Oregon State University; 1U18 FD006445-01, Virginia-Maryland College of Veterinary Medicine; 1U18 FD006859-01, University of Wisconsin-Madison Veterinary Diagnostic Laboratory. Funding Information: This study was funded (PAR-18-604) and performed in collaboration with the Food and Drug Administration’s Veterinary Laboratory Investigation and Response Network (FDA Vet-LIRN) under cooperative agreements 1U18FD006714-01 to L.B.G. and 1U18FD006866-01 to L.W. Additional funding for participating laboratories was as follows: 5U18FD006160-02, Florida Department of Agriculture and Consumer Services; 1U18 FD006444-01, Athens Veterinary Diagnostic Laboratory, The University of Georgia; 1U18 FD006593-01, Michigan State University, Veterinary Diagnostic Laboratory; 1U18 FD006568-01, University of Minnesota, Veterinary Diagnostic Laboratory; 1U18 FD006460-01, University of Missouri, Veterinary Medical Diagnostic Laboratory; 1U18 FD006866-01, 1U18 FD006714-01, Mississippi State University, Veterinary Diagnostic Laboratory; 1U18 FD006555-01, Ohio Animal Disease Diagnostic Laboratory; 1U18FD006671-01, Oklahoma Animal Disease Diagnostic Laboratory, Oklahoma State University; 1U18 FD006719-01, Oregon Veterinary Diagnostic Laboratory, Oregon State University; 1U18 FD006445-01, Virginia-Maryland College of Veterinary Medicine; 1U18 FD006859-01, University of Wisconsin-Madison Veterinary Diagnostic Laboratory. Publisher Copyright: © 2022, Microbiology Society. All rights reserved.

PY - 2022

Y1 - 2022

N2 - There is a growing need for public health and veterinary laboratories to perform whole genome sequencing (WGS) for monitor-ing 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 cor-rectly 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.

AB - There is a growing need for public health and veterinary laboratories to perform whole genome sequencing (WGS) for monitor-ing 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 cor-rectly 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.

KW - One Health

KW - foodborne illness

KW - sequencing accessibility

KW - sequencing quality

UR - http://www.scopus.com/inward/record.url?scp=85123972630&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85123972630&partnerID=8YFLogxK

U2 - 10.1099/mgen.0.000717

DO - 10.1099/mgen.0.000717

M3 - Article

C2 - 35113783

AN - SCOPUS:85123972630

SN - 2057-5858

VL - 8

JO - Microbial genomics

JF - Microbial genomics

IS - 2

M1 - 000717

ER -

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

Abstract

Bibliographical note

Keywords

UN SDGs

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