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Campylobacter sequencing targets public health benefits

By Joe Whitworth+

24-Jan-2014

Photo: University of Liverpool
Photo: University of Liverpool

Campylobacter isolates from two previous studies are to be sequenced by the University of Liverpool and put on a publically accessible database.

Using whole genome sequencing (WGS) at the Centre for Genomic Research, scientists will decode and analyse 510 archived isolates from earlier collections of human faeces.

The project, funded by the Food Standards Agency (FSA) will give scientists a greater understanding of sources and transmission routes associated with human Campylobacter.

Craig Winstanley, professor of microbiology, from the university’s Institute of Infection and Global Health, said the work complements and builds upon a number of other studies. 

“For example, there is Institute for Food Research (IFR) work focused on understanding gene expression in relation to survival in the food chain and infection process,” he told FoodQualityNews.com.

“Our survey will help these researchers to confirm that genes they consider important are present in the most common UK strains associated with human infections.”

Campylobacter sources

Winstanley said it is known that the majority of human cases can be attributed to contaminated poultry, but it is thought there is a significant contribution from sources including the environment.

“In this study we will determine the strain types of Campylobacter associated with community cases of diarrhoea and we can link this with other studies where the strain types associated with sources (such as poultry, cattle, environment etc.) have been determined. 

“This will give us a better idea of the proportion of cases attributable to different sources.”

Illumina and Pacific Biosciences

All isolate genomes will be subjected to sequencing of paired-end libraries using the Illumina HiSeq platform in the project which runs until February 2015.

The genomes of a sub-set of isolates (25) will be improved using a long-read sequencing technique (PacBio by Pacific Biosciences).

Using this combination approach they will construct a genome sequence data-set which will be submitted to a publically accessible database.

Winstanley said the combination of the Illumina and PacBio platforms is ‘ideal’.

“The Illumina HiSeq platform is currently the most cost-effective and reliable method for high-throughput genome sequencing,” he said. 

“Given that there are already a substantial number of reference genomes with which to compare, this approach will be effective for most of the strains. 

“For some more unusual strains, where assembly of the genomes proves difficult, we will obtain new reference genomes using the PacBio platform, which is more expensive but gives longer reads.” 

Genome sequencing

The researchers will extract and analyse multi-locus sequence typing (MLST) data and conduct wider comparative genomics analyses.

The bacterial isolates used are from faecal samples from thousands of people with symptoms of diarrhoea and vomiting during two separate time periods (1993-1996 and 2008-2009).

Winstanley, who is leading the project, said the study would give information on sources and transmission routes and changes between the two study periods

“We will also be able to look for differences between Campylobacter associated with community cases or GP consultations and more severe cases associated with hospitalisations,” he said.

“Most previous studies have not included such a comprehensive survey of community cases or cases identified through GP visits.

“This will help inform policy makers to ensure that interventions are sought where they will have the greatest impact.”

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