Mycobacterium tuberculosis or Yersinia pestis, and for single lineages of more diverse species, for example E. coli O157:H7. However, this approach has potential limitations, particularly when applied to highly diverse species such as Campylobacter jejuni. First, because it requires careful separation of biologically informative SNPs from Dabrafenib relatively common sequencing errors, and second because this approach typically treats dispersed and locally clustered SNPs equally even though the later are likely to be the consequence of horizontal genetic exchange. An alternative to using a reference genome SNP-based approach is to use genes as the units of comparison. In this reference gene based approach, genetic variation within the sample is catalogued one gene at a time by comparison with reference gene sequences, and each new variant is assigned a unique arbitrary allele number in order of description. Both the SNP-based and gene-by-gene approaches rely on reference-based mapping and cannot be used to detect variation in genes that are not present in the reference isolate sequence or locus list. This is not important in analyses based on comparison of a core genome shared among all isolates, but may be less suitable for the discovery of novel genes and functions, and for the examination of the accessory genome composed of genes that vary in presence across isolates of the same population. Here we address this challenge by combining multiple reference genomes to create a single list of genes present in 7 reference genomes from which gene presence and variation can be examined in other bacterial genomes. This list of genes will be hereafter termed the ‘reference pan-genome’ – not to be confused with the true pangenome as it is based on just 7 isolates. This technique is then applied to characterize the genetic variation in Campylobacter jejuni and Campylobacter coli. C. jejuni and C. coli are common constituents of the commensal gut microbiota of various bird and mammal species. Human infection, typically associated with the consumption of contaminated meat or poultry, results in symptoms of severe diarrhea and fever. Campylobacteriosis is currently the most common form of bacterial gastroenteritis in industrialized countries, accounting for an estimated 1 million cases in the UK each year, with an annual economic burden of £500 million. In spite of its public health importance, aspects of the ecology and evolution of Campylobacter remain poorly understood, even though they could have a profound effect on transmission and human infection. For example, it is not fully explained how C. coli and C. jejuni, that have similar host niches and frequently exchange genetic material, differ in terms of their disease epidemiology. Furthermore, within C. jejuni there are lineages that are largely limited to one host and others that are frequently isolated from multiple hosts and are common in human disease. Another potential alternative delivery system for influenza vaccines are bioneedles.