Establishing a Whole Genome Sequence-Based national network for the detection and traceback of Foodborne Pathogens

Establishing a Whole Genome Sequence-Based national network for the detection and traceback of Foodborne Pathogens Marc W. Allard Ph.D. Microbiologist, Division of Microbiology, ORS, Center for Food Safety and Applied Nutrition, (FDA) USA June. 16 th, 2014, efsa Scientific Colloguium Series: Use of Whole Genome Sequencing (WGS) of food-borne pathogens for public health protection

S. Bareilly Outbreak (April-June 2012) FDA1155 SAL2889 Fresh FDA1159 SAL0955 Unknown Cantaloupe SAL3132 USA Environmental FDA713 SAL0949 USA FDA1160 Clinical MD SAL0956 Environmental FDA1145 USA SAL2898 Chili Environmental FDA1107 USA SAL2914 Pabda Powder FDA1141 Thailand SAL2884 Frozen Crab with Fish FDA1150 Bangladesh SAL2439 Frog FDA1157 Claws Sri SAL2908 Lanka Ground FDA1140 Legs Unknown SAL2895 Red Chili FDA1147 Red Pepper SAL2886 USA Fennel Seeds Powder FDA1165 Pakistan SAL2894 Raw United FDA1161 Arab SAL2876 Emirates Whisker Shrimp FDA1163 Vietnam SAL2879 Frozen Raw Esomus FDA1164 Fish Vietnam SAL2887 Sand Goby FDA1117 Swaison Whole SAL2888 Vietnam Frozen FDA1139 Fish Vietnam SAL2890 Kheer Shrimp FDA1123 India SAL2901 Sesame Mix FDA1118 Pakistan SAL2891 Coriander FDA1124 Seeds India SAL2902 Powder FDA1132 India SAL2916 FDA1142 Coconut India SAL2910 Shell-on FDA1200 Shrimp India SAL2917 Cumin Shrimp FDA1129 Sri SAL2911 Lanka Organic Powder FDA1131 India SAL2915 Frozen FDA1207 Black Pepper SAL2925 India Chili FDA1126 Rohu Rish SAL2906 India Ginger Powder FDA1120 India SAL2896 Crushed Powder FDA1138 India SAL2900 Chilis FDA1119 India SAL2893 Frozen Coriander FDA1156 Mexico SAL2892 FDA1121 Fish India SAL2897 Sesame FDA364 Irrigation Water USA Seed FDA1149 India SAL2438 Nonfat Dry ATCC FDA1152 9115 SAL2434 FDA1154 Milk Unknown SAL2436 Poultry FDA1153 Meal SAL2435 USA Poultry Feather FDA1137 Meal SAL2913 USA Feather FDA1130 Meal SAL2912 USA Cayenne Scallops FDA1128 Indonesia SAL2909 Punjabi FDA1204 Pepper India SAL2922 Chili FDA1125 Cheole Spice SAL2905 India Turmeric FDA1115 Powder SAL2882 India Frozen Raw Powder FDA1127 India SAL2907 FDA1113 Peeled Shrimp SAL2880 India Frozen FDA1202 Shrimp India SAL2919 Coriander FDA1201 Shrimp India SAL2918 Coriander Powder FDA1112 India SAL2877 Frozen Bangladesh FDA1203 SAL2921 Frozen Baila Undeveined FDA1205 SAL2923 Shrimp Bangladeshi India Fresh Water Bangladesh FDA1116 SAL2885 Coriander FDA1206 Fish (Bacha) SAL2924 Bangladesh Fish SAL3133 Powder India Stomach FDA1146 Vietnam SAL2903 Hilsa Clinical FDA1148 MD SAL2904 Frozen Rock Lobster Tails Fish FDA1143 Thailand SAL2920 Lobster FDA1144 United Arab SAL2883 Emirates Frozen Whole FDA1114 Tails Taiwan SAL2881 Frozen Raw Tilapia SAL3150 Thailand Shrimp SAL3140 India SAL3130 Clinical NY Clinical SAL3126 NY SAL3139 Clinical MD Clinical SAL3148 MD SAL3128 Clinical NY Clinical SAL3127 NY Clinical SAL3157 MD SAL3131 Clinical MD SAL3155 Clinical NY Clinical SAL3151 MD SAL3129 Clinical NY SAL3141 Clinical NY Clinical SAL3145 MD Clinical SAL3152 NY SAL3158 Clinical NY SAL3153 Clinical NY Clinical SAL3146 NY Clinical SAL3142 NY Clinical SAL3143 NY Clinical SAL3154 NY SAL3144 Clinical NY SAL3156 Clinical NY SAL3125 Clinical NY SAL3149 Clinical NY SAL3147 Clinical MD Clinical NY Clinical NY FDA1114 SAL2881 Frozen Raw Shrimp India SAL3140 Clinical NY SAL3130 Clinical MD SAL3126 Clinical MD SAL3139 Clinical NY SAL3148 Clinical NY SAL3128 Clinical MD SAL3127 Clinical MD SAL3157 Clinical NY SAL3131 Clinical MD SAL3155 Clinical NY SAL3151 Clinical NY SAL3129 Clinical MD SAL3141 Clinical NY SAL3145 Clinical NY SAL3152 Clinical NY SAL3158 Clinical NY SAL3153 Clinical NY SAL3146 Clinical NY SAL3142 Clinical NY SAL3143 Clinical NY SAL3154 Clinical NY SAL3144 Clinical NY SAL3156 Clinical NY SAL3125 Clinical MD SAL3149 Clinical NY SAL3147 Clinical NY FDA1202 SAL2919 Coriander Powder India FDA1203 SAL2921 Frozen Baila Bangladesh FDA1201 SAL2918 Coriander Bangladesh FDA1112 SAL2877 Frozen Undeveined Shrimp India FDA1203 SAL2921 Frozen Baila Bangladesh FDA1206 SAL2924 Fish Stomach Vietnam SAL3133 Clinical MD FDA1146 SAL2903 Hilsa Fish Thailand FDA1148 SAL2904 Frozen Rock Lobster Tails United Arab Emirates FDA1143 SAL2920 Lobster Tails Taiwan FDA1144 SAL2883 Frozen Whole Tilapia Thailand <=5 SNPs FDA1116 SAL2885 Coriander Powder India 20-25 SNPs PFGE Match 110-130 SNPs

Roles for regulatory use of whole genome sequencing 1. Source information 1. Country or state/region of origin 2. Infer a type of food or environment 3. Better target investigational resources 2. Surveillance 3. Risk assessment and modeling 4. Replace traditional bacteriological typing procedures 1. Speed 2. Accuracy 3. Cost

Our Current Model Public FDA, USDA, CDC State, Local, Federal and Foreign Public Health Agencies Academia DATA ANALYSIS NCBI, EMBL DDBJ (Public Access Database) DATA ASSEMBLY AND STORAGE Network of Sequencers DATA ACQUISITION

Network of Sequencers 7 state health depts. + 10 FDA-ORA

Inputs o 1 Miseq system o Sufficient reagents to sequence > 300 genomes per year o Dedicated scientific staff (bioinformatics and/or laboratory support) through Oak Ridge Institute for Science and Education (ORISE) o Bioinformatics and laboratory support, analysis pipeline Deliverables o Minimum ~300 genomes with metadata uploaded to NCBI per annum, minimum 20X coverage o food and environmental related bacterial (prefer Salmonella) isolates

MINIMAL PATHOGEN METADATA (FOODBORNE OUTBREAKS) sample_name organism strain/isolate What Category (attribute_package) 1a) Clinical/Host-associated 1a1) specific_host 1a2) isolation_source 1a3) host-disease OR 1b) Environmental/Food/Other 1b1) isolation_source collection_date Geographic location 6a) geo_loc_name OR 6b) lat_lon collected by When Where Who

Sequences generated by Genometrakr and FDA 1 2013 2010 0 500 1000 1500 2000 2500 9

FDA-State Desktop Pilot called GenomeTrakr - Public Face at NCBI http://www.ncbi.nlm.nih.gov/bioproject/183844 MN and VA most recent partners. Mexico Sinaloa 1 st international partner. SRA completed experiments are ~4,000 records to date. ~500/mo.

Regulatory Genomics and Beyond August 21-22, 2014 Palais des Congrès de Montréal 1001 Place Jean-Paul-Riopelle Montréal, Canada 12

Example of how the network functions Collaboration with NCBI and CDC on real-time Listeria outbreak detection 8 months into project The goal of this project is to type every clinical and food/environmental isolate of Listeria monocytogenes collected in the US. 13

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After second month October 2013 View Trees in NCBI s Genome Work-Bench

Third month November 2013

Current January 2014

Listeria monocytogenes and Support of FDA Compliance Standards > 6 SNPs Isolates from Roos facility, distributed product, and patients who consumed product

Whole-genome sequencing (WGS) of Listeria monocytogenes strains isolated from Roos Foods cheese products has been performed by the FDA and Virginia s Division of Consolidated Laboratory Services. These strains were found to be highly related by WGS to the Listeria strains isolated from patients in this outbreak, adding further confidence that cheese products produced by Roos Foods were a likely source of the outbreak. WGS provides genetic information that allows investigators to rapidly identify differences among isolates. Compared with pulsed-field gel electrophoresis (PFGE), WGS provides clearer distinction between cases and foods that are likely part of a given outbreak and those that are not.

Questions Errol Strain: Errol.Strain@fda.hhs.gov Marc Allard: Marc.Allard@fda.hhs.gov