ABSTRACT

We report here 32 completed closed genome sequences of strains representing 30 serotypes of Salmonella. These genome sequences will provide useful references for understanding the genetic variation within Salmonella enterica serotypes, particularly as references to aid in comparative genomics studies, as well as providing information for improving in silico serotyping accuracy.

ANNOUNCEMENT

Salmonella is the leading cause of bacterial gastroenteritis in North America, with more than 1.7 million cases per annum (1). Public health laboratories are replacing traditional serotyping with whole-genome sequencing (WGS) for faster and more accurate surveillance and outbreak detection (2). The adoption of short-read sequencing technology has generated large amounts of genomic information, but it is fragmented and does not represent the complete DNA sequence of an organism. High-quality genomes are of great value since the use of draft genomes in comparative genomic analyses is complicated due to the inability to distinguish between truly missing sequences and those which were not resolved during the assembly process. Much of the genomic information for Salmonella comes from highly prevalent serotypes, and there is an underrepresentation of the rarer serotypes. Tools for in silico serotype prediction, such as the Salmonella In Silico Typing Resource (SISTR) (3, 4), will benefit from this collection of high-quality reference genomes for 30 serotypes for which no closed genomes were previously available.
As of 9 September 2018, there were 634 fully closed genomes for Salmonella enterica in the NCBI genome database. Unfortunately, the large amounts of raw data available in the Sequence Read Archive (SRA) are composed primarily of Illumina short reads, which cannot readily circularize the Salmonella genome as one contiguous nucleic acid molecule. We have sequenced diverse serotypes of Salmonella using a combination of both Illumina and Oxford Nanopore platforms to produce high-quality de novo closed genomes for public health and comparative genomics applications. This data set represents 30 novel serotypes with 32 closed reference genomes (listed in Table 1).
TABLE 1
TABLE 1 Salmonella enterica strains sequenced in this study, by serotype
SerotypeIsolate no.Molecule typePlasmid nameGenBank accession no.Isolation source speciesIsolation source detailsGenome size (bp)
BertaSA20141895Chromosome CP030005RaccoonNAa4,725,468
 SA20141895PlasmidpSA20141895.1CP030006RaccoonNA67,730
BrandenburgSA20064858Chromosome CP030002PigIntestine4,677,648
 SA20064858PlasmidpSA20064858.1CP030003PigIntestine119,613
 SA20064858PlasmidpSA20064858.2CP030004PigIntestine4,593
 SA20113174Chromosome CP029999PigIntestine4,724,618
 SA20113174PlasmidpSA20113174.1CP030000PigIntestine102,921
 SA20113174PlasmidpSA20113174.2CP030001PigIntestine4,251
CarrauSA20041606Chromosome CP030236NANA4,524,637
 SA20041606PlasmidpSA20041606.1CP030237NANA32,829
ConcordSA20094620Chromosome CP030185NANA4,854,398
 SA20094620PlasmidpSA20094620.1CP030186NANA298,919
 SA20094620PlasmidpSA20094620.2CP030187NANA106,569
 SA20094620PlasmidpSA20094620.3CP030188NANA93,719
 SA20094620PlasmidpSA20094620.4CP030189NANA5,350
GaminaraSA20063285Chromosome CP030288LizardBlood4,834,965
 SA20063285PlasmidpSA20063285.1CP030289LizardBlood117,908
 SA20063285PlasmidpSA20063285.2CP030290LizardBlood3,587
 SA20063285PlasmidpSA20063285.3CP030291LizardBlood1,526
GrumpensisSA20083039Chromosome CP030223NANA4,688,830
 SA20083039PlasmidpSA20083039.1CP030224NANA247,246
II 56:b:1,5SA20053897Chromosome CP029995GeckoFeces4,920,300
 SA20053897PlasmidpSA20053897.1CP029996GeckoFeces87,775
 SA20053897PlasmidpSA20053897.2CP029997GeckoFeces86,128
 SA20053897PlasmidpSA20053897.3CP029998GeckoFeces61,198
II 56:z10:e,n,xSA20011914Chromosome CP029992NANA4,807,680
 SA20011914PlasmidpSA20011914.1CP029993NANA4,593
 SA20011914PlasmidpSA20011914.2CP029994NANA3,904
IIIa 63:g,z51:−SA19981204Chromosome CP029991NANA4,598,348
IIIb 47:r:z53SA20021456Chromosome CP030219NANA5,431,908
 SA20021456PlasmidpSA20021456.1CP030220NANA159,279
 SA20021456PlasmidpSA20021456.2CP030221NANA54,912
 SA20021456PlasmidpSA20021456.3CP030222NANA54,448
IIIb 48:i:zSA20121591Chromosome CP029989SnakeColon5,361,355
 SA20121591PlasmidpSA20121591.1CP029990SnakeColon121,189
IIIb 59:z10:−SA20051472Chromosome CP030026NANA6,125,373
 SA20051472PlasmidpSA20051472.1CP030027NANA169,096
IIIb 60:z52:z53SA20100201Chromosome CP030180NANA5,195,044
IsangiSA20041605Chromosome CP030225NANA4,739,617
 SA20041605PlasmidpSA20041605.1CP030226NANA5,410
 SA20041605PlasmidpSA20041605.2CP030227NANA4,096
 SA20041605PlasmidpSA20041605.3CP030228NANA3,428
 SA20041605PlasmidpSA20041605.4CP030229NANA3,028
IV 45:g,z51:−SA20080453Chromosome CP030194NANA4,651,373
 SA20080453PlasmidpSA20080453.1CP030195NANA38,923
IV 53:z36,z38:−SA20055162Chromosome CP030238NANA4,640,729
KisaraweSA20083530Chromosome CP030203LizardFeces5,062,813
 SA20083530PlasmidpSA20083530.1CP030204LizardFeces138,648
 SA20083530PlasmidpSA20083530.2CP030205LizardFeces33,467
 SA20083530PlasmidpSA20083530.3CP030206LizardFeces27,709
KottbusSA20051528Chromosome CP030211PigLymph node4,719,399
 SA20051528PlasmidpSA20051528.1CP030212PigLymph node4,081
 SA20051528PlasmidpSA20051528.2CP030213PigLymph node2,519
LitchfieldSA20052327Chromosome CP030202ChickenGround meat4,763,586
LivingstoneSA20101045Chromosome CP030233PigIntestine4,729,786
 SA20101045PlasmidpSA20101045.1CP030234PigIntestine94,810
MikawasimaSA20051401Chromosome CP030196HumanStool4,869,528
 SA20051401PlasmidpSA20051401.1CP030197HumanStool141,502
 SA20051401PlasmidpSA20051401.2CP030198HumanStool134,274
 SA20051401PlasmidpSA20051401.3CP030199HumanStool2,729
 SA20051401PlasmidpSA20051401.4CP030200HumanStool2,174
 SA20051401PlasmidpSA20051401.5CP030201HumanStool1,814
MilwaukeeSA19950795Chromosome CP030175NANA4,822,474
 SA19950795PlasmidpSA19950795.1CP030176NANA148,530
 SA19950795PlasmidpSA19950795.2CP030177NANA131,435
NaestvedSA19992307Chromosome CP030207HumanNA4,844,554
 SA19992307PlasmidpSA19992307.1CP030208HumanNA74,577
OhioSA20030575Chromosome CP030181PigLiver4,772,343
 SA20030575PlasmidpSA20030575.1CP030182PigLiver224,430
 SA20030575PlasmidpSA20030575.2CP030183PigFeces94,179
 SA20030575PlasmidpSA20030575.3CP030184PigFeces2,318
 SA20120345Chromosome CP030024PigFeces4,755,436
 SA20120345PlasmidpSA20120345.1CP030025PigFeces100,335
OsloSA20043041Chromosome CP030231NANA4,603,878
 SA20043041PlasmidpSA20043041.1CP030232NANA87,319
ReadingSA20025921Chromosome CP030214BovineMuscle4,882,461
 SA20025921PlasmidpSA20025921.1CP030215BovineMuscle152,311
 SA20025921PlasmidpSA20025921.2CP030216BovineMuscle104,420
RissenSA20104250Chromosome CP030190ChickenMixed organs4,813,547
 SA20104250PlasmidpSA20104250.1CP030191ChickenMixed organs111,887
 SA20104250PlasmidpSA20104250.2P030192ChickenMixed organs4,096
 SA20104250PlasmidpSA20104250.3CP030193ChickenMixed organs2,264
TelelkebirSA20075157Chromosome CP030217NANA4,716,530
 SA20075157PlasmidpSA20075157.1CP030218NANA97,234
UgandaSA20031245Chromosome CP030235NANA4,522,338
YorubaSA20044414Chromosome CP030209NAFeed for fish4,805,225
 SA20044414PlasmidpSA20044414.1CP030210NAFeed for fish92,624
a
NA, not applicable.
Samples were grown on LB plates at 37°C, and genomic DNA was isolated using the Qiagen EZ1 DNA tissue kit on the Qiagen Advanced XL automated instrument, per the manufacturer’s protocol, using 190 μl of G2 buffer with 10 μl of proteinase K. Oxford Nanopore sequencing was performed at the National Microbiology Laboratory (NML) at Guelph (Ontario, Canada), using an Oxford Nanopore MinION sequencer with the default manufacturer protocol for rapid barcoding. Samples were prepared using either SQK-RBK001 or SQK-RBK004 rapid barcoding kits and subsequently run on a FLO-MIN106 R9.4 flow cell. Each multiplexed run produced between 4,719 and 111,488 reads per sample, with the mean read length ranging between 3,485 and 11,880 bp. Albacore v2.1.3, available from Oxford Nanopore, was used to perform demultiplexing, base calling, and quality filtering of the raw reads. Illumina sequencing was done at NML at Guelph on a MiSeq instrument (SY-410-1003; Illumina) using a MiSeq 600-cycle reagent kit v3 (MS-102-3003; Illumina) and Nextera XT DNA library preparation kit (FC-131-1031; Illumina). Each multiplexed run produced between 306,699 and 1,431,596 paired reads per sample. Hybrid de novo assemblies were produced without raw read filtering prior to assembly using the Unicycler pipeline v0.4.3 (5) and were manually reviewed to confirm completeness of the chromosome and any plasmids present. The predicted serotype was determined using the Salmonella In Silico Typing Resource (SISTR) (3, 4) to confirm that the in silico predictions matched the phenotypic serotype determined by the NML Reference Laboratory for Salmonellosis at Guelph.
The high-quality closed reference genomes produced here will be useful for comparative genomics applications, as well as for epidemiological studies on outbreak detection and surveillance of Salmonella.

Data availability.

The genome sequences for the 32 Salmonella isolates produced by the National Microbiology Laboratory Reference Laboratory for Salmonellosis at Guelph have been deposited in NCBI/DDBJ/ENA under BioProject no. PRJNA354244, PRJNA177577, and PRJNA177212. The GenBank accession numbers are all listed in Table 1. The Illumina and Oxford Nanopore raw sequence data in fastq and fast5 formats are also available in the Sequence Read Archive (SRA).

ACKNOWLEDGMENTS

We sincerely thank the following for providing isolates and phenotypic serotyping: Gita Arya, Robert Holtslander, Ketna Mistry, and Roger Johnson of the National Microbiology Laboratory Reference Laboratory for Salmonellosis at Guelph, Public Health Agency of Canada, Guelph, ON, Canada; Vanessa Allen, Anne Maki, and Analyn Peralta of the Enteric Section at the Public Health Ontario Laboratory, Toronto, ON, Canada; Danielle Daignault at the National Microbiology Laboratory, Public Health Agency of Canada, St. Hyacinthe, QC, Canada (ASHQ); Durda Slavic of the Animal Health Laboratory, University of Guelph, Guelph, ON, Canada; Francois-Xavier Weill at Institut Pasteur, Paris, France; Frank Pollari and Rita Finley at FoodNet Canada; and Richard Reid-Smith and Jane Parmley from the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS). We also thank the NCBI PGAP team for their annotation services.
This study was funded by the Public Health Agency of Canada.

REFERENCES

1.
Majowicz SE, Musto J, Scallan E, Angulo FJ, Kirk M, O’Brien SJ, Jones TF, Fazil A, Hoekstra RM, International Collaboration on Enteric Disease “Burden of Illness” Studies. 2010. The global burden of nontyphoidal Salmonella gastroenteritis. Clin Infect Dis 50:882–889.
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Nadon C, Van Walle I, Gerner-Smidt P, Campos J, Chinen I, Concepcion-Acevedo J, Gilpin B, Smith AM, Kam KM, Perez E, Trees E, Kubota K, Takkinen J, Møller Nielsen E, Carleton H, FWD-NEXT Expert Panel. 2017. PulseNet International: vision for the implementation of whole genome sequencing (WGS) for global food-borne disease surveillance. Euro Surveill 22:30544.
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Yoshida CE, Kruczkiewicz P, Laing CR, Lingohr EJ, Gannon VPJ, Nash JHE, Taboada EN. 2016. The Salmonella In Silico Typing Resource (SISTR): an open Web-accessible tool for rapidly typing and subtyping draft Salmonella genome assemblies. PLoS One 11:e0147101.
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Yachison CA, Yoshida C, Robertson J, Nash JHE, Kruczkiewicz P, Taboada EN, Walker M, Reimer A, Christianson S, Nichani A, PulseNet Canada Steering Committee, Nadon C. 2017. The validation and implications of using whole genome sequencing as a replacement for traditional serotyping for a national Salmonella reference laboratory. Front Microbiol 8:1044.
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Wick RR, Judd LM, Gorrie CL, Holt KE. 2017. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 13:e1005595.

Information & Contributors

Information

Published In

cover image Microbiology Resource Announcements
Microbiology Resource Announcements
Volume 7Number 171 November 2018
eLocator: 10.1128/mra.01232-18
Editor: Christina A. Cuomo, Broad Institute of MIT and Harvard University

History

Received: 17 September 2018
Accepted: 9 October 2018
Published online: 1 November 2018

Contributors

Authors

National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
Kira Liu
National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
Simone Gurnik
National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
Catherine Yoshida
National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
National Microbiology Laboratory, Public Health Agency of Canada, Toronto, Ontario, Canada

Editor

Christina A. Cuomo
Editor
Broad Institute of MIT and Harvard University

Notes

Address correspondence to Kyrylo Bessonov, [email protected].

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