WGS and geographic mapping traces outbreak source to India

By Joseph James Whitworth

- Last updated on GMT

Picture: FDA/Flickr. Multistate outbreak of Salmonella Bareilly infections
Picture: FDA/Flickr. Multistate outbreak of Salmonella Bareilly infections

Related tags Salmonella enterica

Whole Genome Sequencing (WGS) and geographic mapping clearly improves source tracking and surveillance of foodborne outbreaks, according to researchers.

A study combined the methods to trace the origin of Salmonella Bareilly isolates collected in 2012 during an outbreak associated with scraped tuna imported from India.

Researchers sequenced the complete genome of 100 S.​ Bareilly isolates from patients who ate contaminated product, natural sources, and unrelated historically and geographically disparate foods.

Improving tracking and surveillance

By projecting the phylogeny onto a globe using SUPRAMAP, a web application, an interactive map can be produced for exploring connections between outbreak cases and mutations along each branch in the tree.

Phylogenetic analysis of WGS data indicated patients in Maryland and New York were infected from sources originating in India.

“By merging comparative genomic analysis with geographical mapping tools, we were able to generate a transmission graph that revealed where S. Bareilly pathogens may have originated," ​said the researchers

“These new technologies enabled traceback to the contamination source with a high degree of certainty and allowed us to better understand S. Bareilly’s pathogen transmission network.”

Public health authorities investigated a multistate outbreak of Salmonella enterica subspecies enterica serovar Bareilly and S. Nchanga infections with illness dates between January 1 and July 7, 2012.

The data set was 100 S. Bareilly isolates from clinical, food, feed and environmental sources with 41 of them collected during the investigation of the tuna scrape-associated outbreak in 2012.

A single isolate, S. Bareilly CFSAN000189, was sequenced on the Pacific Biosciences (PacBio) RS II Sequencer.

Most isolates (96) were sequenced using Illumina’s MiSeq platform. Five were sequenced using an Ion Torrent (PGM) sequencing system from Life Technologies with the 200-bp reads chemistry.

Outbreak cases

A total of 425 cases were reported in 28 states and the District of Colombia of which 410 (96.5%) were found to be caused by S. Bareilly infection.

Investigations linked this outbreak to a frozen, raw yellowfin tuna product (“tuna scrape”).

This product had been marketed as “Nakaochi Scrape” by an Indian corporation and used to make spicy tuna sushi for restaurants and grocery stores.

Some strains of S​. Bareilly are clonal and can be detected in numerous sites throughout Southeast Asia.

This makes epidemiological traceback using conventional tools such as pulsed field gel electrophoresis (PFGE) difficult, which does not provide the level of resolution necessary to distinguish outbreak strains from clonally-related S​. Bareilly isolates previously from other sources.

Advances in WGS and geographic information systems software enable researchers to integrate phylogenetic trees (based on single-nucleotide polymorphism (SNP) data) with the metadata associated with isolates – such as date of collection and latitude and longitude coordinates.

Phylogenetic character evolution from WGS data and geographic metadata was used to create a transmission network in the study. 

“Such networks could be used to identify geographic locations important for historical transmission and spread of S. Bareilly and can enable food producers and public health officials to target interventions at those places where they may have the most impact for improving food safety​,” said the researchers.

Source: Journal of Infectious Diseases

Online, ahead of print DOI: 10.1093/infdis/jiv297

Tracing Origins of the Salmonella Bareilly strain causing a Foodborne Outbreak in the United States​”

Authors: Maria Hoffmann, Yan Luo, Steven R. Monday, Narjol Gonzales-Escalona, Andrea R. Ottesen, Tim Muruvanda, Charles Wang, George Kastanis, Christine Keys, Daniel Janies, Izzet F. Senturk, Umit V. Catalyurek, Hua Wang, Thomas S. Hammack, William J. Wolfgang, Dianna Schoonmaker-Bopp, Alvina Chu, Robert Myers, Julie Haendiges, Peter S. Evans, Jianghong Meng, Errol A. Strain, Marc W. Allard, and Eric W. Brown

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