The Benefits of Whole Genome Sequencing for Foodborne Outbreak Investigation from the Perspective of a National Reference Laboratory in a Smaller Country
Abstract
:1. Introduction
2. Materials and Methods
2.1. Conventional Methods Applied for the Initial Outbreak Investigation
2.2. Retrospective WGS-Based Outbreak Analysis
3. Results
3.1. Description of the Selected Outbreaks and Isolates
3.2. Comparing Isolate Characterization Using WGS and Conventional Methods
3.3. Comparison of the Phylogenetic Performance between WGS and Conventional Methods in Resolving Relatedness
4. Discussion
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Isolate Reference | Isolation Date (dd/mm/yyyy) | Origin | Conventional Methods | WGS | |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Serotype | Virulence Genes | AMR | Relation to Outbreak | Serotype | Virulence Genotype | AMR Genotype | Relation to Outbreak | ||||||||||||||||||||||||||||||
stx1 | stx2 | eae | ehxA | aggR | aaiC | stx1 | stx2 | eae | ehxA | aggR | aaiC | katP | toxB | astA | esp | gad | nle | tir | iss | etpD | iha | tccP | blaTEM-1B | aph(3’)-Ia | str | sul2 | tetA | dfrA8 | mdfA | ||||||||
EH2165 | 06/06/2012 | Human | O157:H7 | a | a | + | + | - | - | S | O | O157:H7 | a | a | + | + | - | - | + | + | + | A, B, F, J, P | + | A, B, C | + | + | + | + | + | - | - | - | - | - | - | + | O |
EH2169 | 07/06/2012 | Human | O157:H7 | a | a | + | + | - | - | S | O | O157:H7 | a | a | + | + | - | - | + | + | + | A, B, F, J, P | + | A, B, C | + | + | + | + | + | - | - | - | - | - | - | + | O |
EH2170 | 12/06/2012 | Human | O157:H7 | a | a | + | + | - | - | S | O | O157:H7 | a | a | + | + | - | - | + | + | + | A, B, F, J, P | + | A, B, C | + | + | + | + | + | - | - | - | - | - | - | + | O |
EH2171 | 13/06/2012 | Human | O157:H7 | a | a | + | + | - | - | S | O | O157:H7 | a | a | + | + | - | - | + | + | + | A, B, F, J, P | + | A, B, C | + | + | + | + | + | - | - | - | - | - | - | + | O |
EH2174 | 12/06/2012 | Human | O157:H7 | a | a | + | + | - | - | S | O | O157:H7 | a | a | + | + | - | - | + | + | + | A, B, F, J, P | + | A, B, C | + | + | + | + | + | - | - | - | - | - | - | + | O |
EH2176 | 08/06/2012 | Human | O157:H7 | a | a | + | + | - | - | S | O | O157:H7 | a | a | + | + | - | - | + | + | + | A, B, F, J, P | + | A, B, C | + | + | + | + | + | - | - | - | - | - | - | + | O |
EH2177 | 08/06/2012 | Human | O157:H7 | a | a | + | + | - | - | S | O | O157:H7 | a | a | + | + | - | - | + | + | + | A, B, F, J, P | + | A, B, C | + | + | + | + | + | - | - | - | - | - | - | + | O |
EH2178 | 13/06/2012 | Human | O157:H7 | a | a | + | + | - | - | S | O | O157:H7 | a | a | + | + | - | - | + | + | + | A, B, F, J, P | + | A, B, C | + | + | + | + | + | - | - | - | - | - | - | + | O |
EH2179 | 14/06/2012 | Human | O157:H7 | a | a | + | + | - | - | S | O | O157:H7 | a | a | + | + | - | - | + | + | + | A, B, F, J, P | + | A, B, C | + | + | + | + | + | - | - | - | - | - | - | + | O |
EH2180 | 14/06/2012 | Human | O157:H7 | a | a | + | + | - | - | S | O | O157:H7 | a | a | + | + | - | - | + | + | + | A, B, F, J, P | + | A, B, C | + | + | + | + | + | - | - | - | - | - | - | + | O |
EH2181 | 14/06/2012 | Human | O157:H7 | a | a | + | + | - | - | S | O | O157:H7 | a | a | + | + | - | - | + | + | + | A, B, F, J, P | + | A, B, C | + | + | + | + | + | - | - | - | - | - | - | + | O |
EH2182 | 14/06/2012 | Human | O157:H7 | a | a | + | + | - | - | S | O | O157:H7 | a | a | + | + | - | - | + | + | + | A, B, F, J, P | + | A, B, C | + | + | + | + | + | - | - | - | - | - | - | + | O |
EH2183 | 19/06/2012 | Human | O157:H7 | a | a | + | + | - | - | S | O | O157:H7 | a | a | + | + | - | - | + | + | + | A, B, F, J, P | + | A, B, C | + | + | + | + | + | - | - | - | - | - | - | + | O |
EH2189 | 22/06/2012 | Human | O157:H7 | a | a | + | + | - | - | S | O | O157:H7 | a | a | + | + | - | - | + | + | + | A, B, F, J, P | + | A, B, C | + | + | + | + | + | - | - | - | - | - | - | + | O |
EH2192 | 26/06/2012 | Human | O157:H7 | a | a | + | + | - | - | S | O | O157:H7 | a | a | + | + | - | - | + | + | + | A, B, F, J, P | + | A, B, C | + | + | + | + | + | - | - | - | - | - | - | + | O |
EH2193 | 26/06/2012 | Human | O157:H7 | a | a | + | + | - | - | S | O | O157:H7 | a | a | + | + | - | - | + | + | + | A, B, F, J, P | + | A, B, C | + | + | + | + | + | - | - | - | - | - | - | + | O |
EH2194 | 02/07/2012 | Human | O157:H7 | a | a | + | + | - | - | S | O | O157:H7 | a | a | + | + | - | - | + | + | + | A, B, F, J, P | + | A, B, C | + | + | + | + | + | - | - | - | - | - | - | + | O |
TIAC1150 | 27/06/2012 | Filet americain | O157:H7 | a * | a * | + | + * | - | - | S * | O | O157:H7 | a | a | + | + | - | - | + | + | + | A, B, F, J, P | + | A, B, C | + | + | + | + | + | - | - | - | - | - | - | + | O |
TIAC1151 | 19/06/2012 | Filet americain | O157:H7 | a * | a * | + | + * | - | - | S * | O | O157:H7 | a | a | + | + | - | - | + | + | + | A, B, F, J, P | + | A, B, C | + | + | + | + | + | - | - | - | - | - | - | + | O |
TIAC1152 | 19/06/2012 | Filet americain | O157:H7 | a * | a * | + | + * | - | - | S * | O | O157:H7 | a | a | + | + | - | - | + | + | + | A, B, F, J, P | + | A, B, C | + | + | + | + | + | - | - | - | - | - | - | + | O |
TIAC1153 | 18/06/2012 | Carcass swab | O157:H7 | a * | c * | + | + * | - | - | AMP, KAN, STR, SUL, SXT, TET * | N | O157:H7 | a | c | + | + | - | - | + | + | + | A, B, F, J, P | + | A, B, C | + | + | + | + | + | + | + | A, B | + | + | + | + | N |
Isolate Reference | Isolation Date (dd/mm/yyyy) | Origin | Conventional Methods | WGS | |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Serotype | Virulence Genes | AMR | Relation to Outbreak | Serotype | Virulence Genotype | AMR Genotype | Relation to Outbreak | ||||||||||||||||||||||||||||||
stx1 | stx2 | eae | ehxA | aggR | aaiC | stx1 | stx2 | eae | ehxA | aggR | aaiC | katP | toxB | astA | esp | gad | nle | tir | iss | etpD | iha | tccP | blaTEM-1B | aadA1 | str | tetA | dfrA1 | sul | mdfA | ||||||||
EH2264 | 15/05/2013 | Human | O157:H7 | - | a | + | + | - | - | S | N | O157:H7 | - | a | + | + | - | - | + | + | + | A, B, F, J, P | + | A, B, C | + | + | + | + | + | - | - | - | - | - | - | + | N |
EH2268 | 28/05/2013 | Human | O157:H7 | - | a | + | + | - | - | S | N | O157:H7 | - | a | + | + | - | - | + | + | + | A, B, F, J, P | + | A, B, C | + | + | + | + | + | - | - | - | - | - | - | + | N |
EH2272 | 08/06/2013 | Human | O157:H7 | - | a | + | + | - | - | S | ? | O157:H7 | - | a | + | + | - | - | + | + | + | A, B, F, J, P | + | A, B, C | + | + | + | + | + | - | - | - | - | - | - | + | O * |
EH2274 | 13/06/2013 | Human | O157:H7 | - | a | + | + | - | - | S | O* | O157:H7 | - | a | + | + | - | - | + | + | + | A, B, F, J, P | + | A, B, C | + | + | + | + | + | - | - | - | - | - | - | + | O * |
EH2275 | 13/06/2013 | Human | O157:H7 | - | a | + | + | - | - | S | O * | O157:H7 | - | a | + | + | - | - | + | + | + | A, B, F, J, P | + | A, B, C | + | + | + | + | + | - | - | - | - | - | - | + | O * |
EH2277 | 18/06/2013 | Human | O157:H7 | - | a | + | + | - | - | S | O * | O157:H7 | - | a | + | + | - | - | + | + | + | A, B, F, J, P | + | A, B, C | + | + | + | + | + | - | - | - | - | - | - | + | O * |
EH2278 | 18/06/2013 | Human | O157:H7 | - | a | + | + | - | - | S | O * | O157:H7 | - | a | + | + | - | - | + | + | + | A, B, F, J, P | + | A, B, C | + | + | + | + | + | - | - | - | - | - | - | + | O * |
EH2279 | 18/06/2013 | Human | O157:H7 | - | a | + | + | - | - | S | O * | O157:H7 | - | a | + | + | - | - | + | + | + | A, B, F, J, P | + | A, B, C | + | + | + | + | + | - | - | - | - | - | - | + | O * |
EH2280 | 18/06/2013 | Human | O157:H7 | - | a | + | + | - | - | S | O * | O157:H7 | - | a | + | + | - | - | + | + | + | A, B, F, J, P | + | A, B, C | + | + | + | + | + | - | - | - | - | - | - | + | O * |
EH2281 | 20/06/2013 | Human | O157:H7 | - | a | + | + | - | - | S | O * | O157:H7 | - | a | + | + | - | - | + | + | + | A, B, F, J, P | + | A, B, C | + | + | + | + | + | - | - | - | - | - | - | + | O * |
EH2285 | 28/06/2013 | Human | O157:H7 | - | a | + | + | - | - | AMP, STR, TET, SXT | O * | O157:H7 | - | a | + | + | - | - | + | + | + | A, B, F, J, P | + | A, B, C | + | + | + | + | + | + | + | A, B | + | + | 1, 2 | + | O * |
EH2295 | 12/07/2013 | Human | O157:H7 | - | a | + | + | - | - | S | N | O157:H7 | - | a | + | + | - | - | + | + | + | A, B, F, J, P | + | A, B, C | + | + | + | + | + | - | - | - | - | - | - | + | N |
EH2297 | 16/07/2013 | Human | O157:H7 | - | a | + | + | - | - | S | O | O157:H7 | - | a | + | + | - | - | + | + | + | A, B, F, J, P | + | A, B, C | + | + | + | + | + | - | - | - | - | - | - | + | O |
EH2299 | 18/07/2013 | Human | O157:H7 | - | a | + | + | - | - | S | ? | O157:H7 | - | a | + | + | - | - | + | + | + | A, B, F, J, P | + | A, B, C | + | + | + | + | + | - | - | - | - | - | - | + | N |
EH2308 | 31/07/2013 | Human | O157:H7 | a | a | + | + | - | - | S | N | O157:H7 | a | a | + | + | - | - | + | + | + | A, B, F, J, P | + | A, B, C | + | + | + | + | + | - | - | - | - | - | - | + | N |
TIAC1903 | 01/07/2013 | Filet americain | O157:H7 | - | a * | + | + * | - * | - * | S * | O | O157:H7 | - | a | + | + | - | - | + | + | + | A, B, F, J, P | + | A, B, C | + | + | + | + | + | - | - | - | - | - | - | + | O |
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Nouws, S.; Bogaerts, B.; Verhaegen, B.; Denayer, S.; Crombé, F.; De Rauw, K.; Piérard, D.; Marchal, K.; Vanneste, K.; Roosens, N.H.C.; et al. The Benefits of Whole Genome Sequencing for Foodborne Outbreak Investigation from the Perspective of a National Reference Laboratory in a Smaller Country. Foods 2020, 9, 1030. https://doi.org/10.3390/foods9081030
Nouws S, Bogaerts B, Verhaegen B, Denayer S, Crombé F, De Rauw K, Piérard D, Marchal K, Vanneste K, Roosens NHC, et al. The Benefits of Whole Genome Sequencing for Foodborne Outbreak Investigation from the Perspective of a National Reference Laboratory in a Smaller Country. Foods. 2020; 9(8):1030. https://doi.org/10.3390/foods9081030
Chicago/Turabian StyleNouws, Stéphanie, Bert Bogaerts, Bavo Verhaegen, Sarah Denayer, Florence Crombé, Klara De Rauw, Denis Piérard, Kathleen Marchal, Kevin Vanneste, Nancy H. C. Roosens, and et al. 2020. "The Benefits of Whole Genome Sequencing for Foodborne Outbreak Investigation from the Perspective of a National Reference Laboratory in a Smaller Country" Foods 9, no. 8: 1030. https://doi.org/10.3390/foods9081030