Abstract
PulseNet International is a global network dedicated to laboratory-based surveillance for food-borne diseases. The network comprises the national and regional laboratory networks of Africa, Asia Pacific, Canada, Europe, Latin America and the Caribbean, the Middle East, and the United States. The PulseNet International vision is the standardised use of whole genome sequencing (WGS) to identify and subtype food-borne bacterial pathogens worldwide, replacing traditional methods to strengthen preparedness and response, reduce global social and economic disease burden, and save lives. To meet the needs of real-time surveillance, the PulseNet International network will standardise subtyping via WGS using whole genome multilocus sequence typing (wgMLST), which delivers sufficiently high resolution and epidemiological concordance, plus unambiguous nomenclature for the purposes of surveillance. Standardised protocols, validation studies, quality control programmes, database and nomenclature development, and training should support the implementation and decentralisation of WGS. Ideally, WGS data collected for surveillance purposes should be publicly available, in real time where possible, respecting data protection policies. WGS data are suitable for surveillance and outbreak purposes and for answering scientific questions pertaining to source attribution, antimicrobial resistance, transmission patterns, and virulence, which will further enable the protection and improvement of public health with respect to food-borne disease.
Highlights
Almost one in 10 people in the world become ill every year due to consumption of contaminated food; diarrhoeal diseases are the most common cause of illness, with 550 million cases and 230,000 deaths every year [1]
This paper provides considerations of the critical technical and practical aspects of Whole genome sequencing (WGS) from the perspective of standardised international laboratorybased surveillance and the prerequisites for routine implementation in public health
To meet the needs of real-time surveillance, PulseNet International will standardise WGS-based subtyping using extended multilocus sequence typing (MLST)-based approaches; whole genome multilocus sequence typing (wgMLST). This delivers optimal resolution and epidemiological concordance while providing unambiguous nomenclature. It is computationally efficient and realistic for most public health laboratories to use on a daily basis
Summary
Almost one in 10 people in the world become ill every year due to consumption of contaminated food; diarrhoeal diseases are the most common cause of illness, with 550 million cases and 230,000 deaths every year [1]. The mission of PulseNet International is to implement standardised genotyping methods and share information in real-time within regional and national laboratory networks to support surveillance and outbreak response enabling the direct comparison of inter-laboratory data irrespective of geography. Assembling is the process of placing all of the reads together in the correct order to create a small number of contiguous sequences, known as contigs (FASTA format) This can be done using a known reference sequence (closed genome) to guide the assembly, or it can be done de novo (draft genome), i.e. without prior knowledge of the expected order. The latter is computationally relatively demanding for the four main species involved in food-borne diseases: Salmonella spp, Campylobacter spp, Listeria monocytogenes and Shiga toxin-producing Escherichia coli [17]. Due to the short length of the individual reads compared with repetitive regions, a genome for these species is rarely fully assembled (closed genome)
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