TABLE 5.
The use of whole genome sequencing (WGS) for epidemiological purposes (chosen listeriosis outbreaks).
| Year | Location | Source | No. of cases (No. of deaths) | WGS analysis | References | |
|---|---|---|---|---|---|---|
| United States | 2014 | Multistate | FNAO: mung bean sprouts | 5 (2) | 4b; high genetic relationship of mung bean sprout isolates, environmental isolates collected in the production plant with sequences of strains isolated from patients | Centers for Disease Control and Prevention (2015b) |
| 2014–2015 | 12 states | FNAO: caramel apples | 35 (7) | - The WGS distinguished two isolates of L. monocytogenes (one in each cluster) with a high degree of similarity (PFGE - no distinction) | Centers for Disease Control and Prevention (2015a) | |
| - WGS analysis showed that L. monocytogenes isolates from whole apples produced by Bidart Bros collected along the distribution chain were strongly related to the outbreak strains | ||||||
| - It is estimated that the use of WGS shortened the epidemic by 1 week | ||||||
| 2015 | 10 states | Soft cheeses distributed by Karoun dairies | 30 (3) | - WGS gives a more detailed DNA fingerprint than PFGE | Centers for Disease Control and Prevention (2017a) | |
| - WGS - four different PFGE fingerprints were genetically closely related to the first PFGE fingerprint | ||||||
| 2016 | Two states | Raw milk | 2 (1) | WGS - close genetic relationship of L. monocytogenes strains isolated from two patients and a milk sample | Centers for Disease Control and Prevention (2016b) | |
| 2016 | 4 states | FNAO: frozen vegetables | 9 (3) | The frozen corn isolate of L. monocytogenes was shown to be closely related to the eight patient isolates, and the frozen pea isolate to the patient isolate was shown to be closely related to the eight patient isolates | Centers for Disease Control and Prevention (2016c) | |
| 2016 | 9 states | FNAO: packaged salads | 19 (1) | - More fingerprint than PFGE | Centers for Disease Control and Prevention (2016d) | |
| - WGS analysis showed a close genetic relationship between isolates from patients in Canada and patient isolates in the United States | ||||||
| 2017 | 4 states | Soft raw milk cheese | 8 (2) | WGS analysis of patient isolates revealed a common source of L. monocytogenes | Centers for Disease Control and Prevention (2017b) | |
| 2019 | 5 states | Hard-boiled eggs | 8 (1) | The WGS showed that the bacteria in the environmental sample were genetically closely related to bacteria from sick people | Centers for Disease Control and Prevention (2020a) | |
| 2020 | 4 states | Deli meats | 12 (1) | Close genetic relationship of strains isolated from sick people | Centers for Disease Control and Prevention (2021) | |
| 2022 | 11 states | Ice cream | 28 (1) | WGS analysis showed that L. monocytogenes isolates collected from the ice cream and production environment were the source of the outbreak | Chen et al. (2017); Centers for Disease Control and Prevention (2022b) | |
| 2022 | 8 states | FNAO: packaged salads | 10 (1) | The WGS analysis enabled the detection of outbreak of L. monocytogenes | Centers for Disease Control and Prevention (2022c) | |
| Europe | 2015–2018 | Austria, Denmark, Finland, Sweden, The United Kingdom | FNAO: frozen corn | 41 (6) | The WGS analysis enabled the detection of a multi-country outbreak of L. monocytogenes | European Centre for Disease Prevention and Control (2018b) |
| Since 2015 | Denmark, Germany, France | RTE salmon products | 12 (4) | The WGS analysis enabled the detection of a multi-country outbreak of L. monocytogenes | European Centre for Disease Prevention and Control (2018a) | |
| 2014–2019 | Denmark, Estonia, Finland, France, Sweden | Cold-smoked fish products | 22 (5) | The WGS analysis enabled the detection of a multi-country outbreak of L. monocytogenes | European Centre for Disease Prevention and Control (2019b) | |
| 2017–2019 | Netherlands, Belgium | RTE meat products | 21 (3) | The WGS analysis enabled the detection of a multi-country outbreak of L. monocytogenes (detected in wholesale and retail in four countries) | European Centre for Disease Prevention and Control (2019c) | |
| 2019 | Spain | Chilled roasted pork meat product | 222 (3) | WGS analysis of L. monocytogenes isolates showed that human and food isolates share the same sequence | World Health Organization (2019) | |
| Africa | 2017–2018 | Republic of South Africa | RTE processed meat products | 1,024 (200) | - WGS analysis of isolates from a large subgroup of patients showed the same sequence type in a commonly consumed RTE processed meat product and in the manufacturer’s processing environment | NSW Department of Primary Industries (2018); World Health Organization (2018c) |
| - All L. monocytogenes positives were further identified as the outbreak WGS strain belonging to MLST240 | ||||||
| Australia | 2018 | Australia (New South Wales, Victoria, Queensland, Tasmania) | FNAO: rockmelons | 20 (7) | WGS analysis reported two cases in Singapore reported to be genetically linked to the Australian outbreak strain | Das (2019) |
WGS, whole genome sequencing; PFGE, Pulsed-field gel electrophoresis; RTE, ready-to-eat; FNAO, Food of non-animal origin.