Table 2.
Examplesa of published high throughput sequencing based investigations of foodborne pathogen (FBP) outbreaks.
| Type of FBP | Isolates/strains or community analyzed? | Material sequenced | Sequencing technology applied | Sequencing and bioinformatics approaches | Where and when | References |
|---|---|---|---|---|---|---|
| BACTERIAL FBPs | ||||||
| E. coli (STECb) serotype O157:H7 | Isolates | 70 isolates from two outbreaks complemented with isolates from sporadic cases | HiSeq2500 (Illumina), 200PEc | Whole genome sequencing (WGS) of single isolates followed by mapping to reference genome and single nucleotide polymorphism (SNP) analysis | UK, 2013 | Jenkins et al., 2015 |
| O157:H7 | Isolates | 29 isolates, 24 isolates from an outbreak, 5 unrelated cases | MiSeq (Illumina), 150PE | WGS of single isolates followed by de novo assembly and reference-based SNP analysis | US, 2001–2012 | Turabelidze et al., 2013 |
| O157:H7 | Isolates | 16 isolates, 8 from humans, 8 from animals | GS FLX (Roche) and GAIIx (Illumina) | WGS of single isolates followed by de novo assembly and reference-based SNP analysis | UK, 2009 | Underwood et al., 2013 |
| O157:H7 | Isolates | 105 isolates, 10 human isolates from an outbreak, 95 human isolates from sporadic cases | Ion Torrent PGM (Life technologies) | WGS of single isolates followed by mapping to reference genome and single nucleotide polymorphism (SNP) analysis | UK, 2007–2012 | Holmes et al., 2015 |
| Multiple STEC serotypes | Isolates | 46 isolates, 6 isolates from humans from an outbreak, 40 human isolates from sporadic cases | Ion Torrent PGM | WGS of single isolates followed by multi-locus sequence typing (MLST), k-mer and phylogenetic analysis against up to 5,029 bacterial genomes | DK, 2012 | Joensen et al., 2014 |
| O104:H4 | Communities | 45 clinical human fecal samples | MiSeq 151PE and HiSeq 2500 151PE rapid mode shotgun metagenomics yielding from 8.6 × 106 to 4.4 × 107 reads per sample | Retrospective study applying shotgun metagenomics, followed by in silico subtraction of human DNA and de novo assembly to create environmental gene tags (EGTs). EGTs identified in more than 20 fecal samples were selected for further analysis, and EGTs identified in fecal samples from healthy humans were discarded. Reference-based mapping and phylogenetic analysis combined with further assembly to functionally annotate the EGTs and reconstruct the outbreak strain genome. Verification of results by comparison to the previously sequenced genome of the outbreak strain | Germany/Europe, 2011 | Loman et al., 2013 |
| Listeria monocytogenes | Isolates | 2 isolates with one band difference on PFGE | GS FLX and GAIIx | WGS of single isolates followed by de novo assembly and gap closure | Canada, 2008 | Gilmour et al., 2010 |
| L. monocytogenes | Isolates | 5 isolates, three from humans and two environmental isolates associated to one outbreak | Ion Torrent PGM | WGS of single isolates followed by de novo assembly and scaffolding against an assembled reference genome | Australia, 2013 | Wang et al., 2015b |
| L. monocytogenes | Isolates | 18 isolates, 7 human, 10 food isolates, 1 control isolate | MiSeq, 75PE, 150PE and 250PE | WGS of single isolates followed by de novo assembly and gene-by-gene analysis (extended MLST) | Austria 2011–2013 | Schmid et al., 2014 |
| Salmonella enterica serovar Typhimurium | Isolates | 57 isolates from 5 outbreaks | MiSeq, 250PE | WGS of single isolates followed by de novo assembly and mapping based SNP analysis | Australia, 2006–2012 | Octavia et al., 2015 |
| Serovar Typhimurium | Isolates | 61 isolates, 21 human and 5 food isolates related to an outbreak and additional 35 isolates | HiSeq2500 | WGS of single isolates followed by mapping based SNP analysis | UK, 2012 | Ashton et al., 2015 |
| Serovar Enteritidis | Isolates | 55 isolates, 28 isolates from 7 outbreaks, 27 isolates from sporadic cases | MiSeq, 250PE | WGS of single isolates followed by mapping based SNP analysis | US, 2001–2012 | Taylor et al., 2015 |
| Serovar Enteritidis | Isolates | 6 isolates, 3 human and 3 food isolates | HiSeq2000 (Illumina), 100PE | WGS of single isolates followed by de novo assembly and mapping based SNP analysis | Belgium, 2014 | Wuyts et al., 2015 |
| Serovars Typhimurium, Enteritidis and Derby | Isolates | 47 isolates, 26 isolates from 9 outbreaks, 21 isolates from sporadic cases | GAIIx, 101PE | WGS of single isolates followed by reference free de novo assembly, complemented with reference based pan-genome, SNP and k-mer analysis | Denmark, 2000–2010 | Leekitcharoenphon et al., 2014 |
| VIRAL FBPs | ||||||
| Hepatitis A virus (HAV) | Isolated HAV communities | HAV communities from clinical serum and fecal samples from 120 patients associated with a single outbreak | No data on sequencing approach except fragment size (315 bp) | Metataxonomics, i.e., amplicon sequencing of VP1/P2B region of HAV, followed by mapping to HAV genotype reference sequences, complemented with phylogenetic analysis | USA, 2013 | Collier et al., 2014 |
| HAV | Isolates and communities | Two food samples from two apparently unrelated HAV outbreaks | RNAseq combined with amplicon sequencing (MiSeq; 250PE) | Four amplicons, partially overlapping, covered the entire HAV genome. Genome assembly followed by genotyping by mapping to HAV reference genomes | Italy, 2013 | Chiapponi et al., 2014 |
| Rotavirus | Community | One clinical fecal sample from a small outbreak | RNAseq on MiSeq (120PE), approximately 1 × 106 reads | Genotyping by mapping to rotavirus reference genomes | Japan, 2012 | Mizukoshi et al., 2014 |
| FUNGAL FBPs | ||||||
| Mucor circinelloides f. circinelloides | Isolates | Seven isolates from outbreak associated food (yogurt) | WGS (HiSeq2000 100PE and 100MPd) and amplicon sequencing (targets specified but no details on sequencing approach) | Metataxonomic MLST approach to species and sub-species (formae) identification, targeting three loci (ribosomal internal transcribed spacer and partial large subunit RNA gene, and RNA polymerase subunit gene), complemented with phylogenetic analysis. Whole genome comparison by genome assembly and mapping to genome sequences of two other M. circinelloides isolates | USA, 2013 | Lee et al., 2014 |
| PARASITIC FBPs | ||||||
| Kudoa septempunctata | Community | Frozen filet of outbreak associated food (fish), and vomit samples from patients associated with the outbreak | RNAseq on GAII (80PE) complemented with Sanger amplicon sequencing of DNA (1.1 kbp fragment of 18S rRNA gene) | In silico subtraction of reads from the food sample against fish genome followed by mapping of remaining reads for taxonomic classification. Metataxonomic analysis of 18S rRNA gene sequence by mapping to multi-species 18S rRNA gene database | Japan, 2008–2010 | Kawai et al., 2012 |
a
The examples are further described and discussed in the main text of this review.
b
STEC, shiga-toxin producing E. coli.
c
200PE refers to the use of paired-end sequencing with a read length of 200 bp.
d
100MP refers to the use of mate-pair sequencing with a read length of 100 bp