Abstract
As a leading cause of bacterial-derived gastroenteritis worldwide, Campylobacter jejuni has a significant impact on human health in both the developed and developing worlds. Despite its prevalence as a human pathogen, the source of these infections remains poorly understood due to the mutation frequency of the organism and past limitations of whole genome analysis. Recent advances in both whole genome sequencing and computational methods have allowed for the high-resolution analysis of intraspecies diversity, leading multiple groups to postulate that these approaches may be used to identify the sources of Campylobacter jejuni infection. To address this hypothesis, our group conducted a regionally and temporally restricted sampling of agricultural and environmental Campylobacter sources and compared isolated C. jejuni genomes to those that caused human infections in the same region during the same time period. Through a network analysis comparing genomes from various sources, we found that human C. jejuni isolates clustered with those isolated from cattle and chickens, indicating these as potential sources of human infection in the region.
Highlights
As a leading cause of bacterial-derived gastroenteritis worldwide, Campylobacter species have a significant impact on human health (Kaakoush et al, 2015; Crofts et al, 2018) with approximately 96 million global cases (Kirk et al, 2015) and 1.3 million cases in the United States, annually (Fitzgerald et al, 2016)
Pulse-field gel electrophoresis (PFGE) was highly impactful in identifying foodborne outbreaks and performing bacterial source-tracking of E. coli and Salmonella serotypes (Johnson et al, 1995; Fugett et al, 2007). Since this method relies on gel-based resolution of genomic restriction fragments, it can fail to discriminate between strains of bacterial species that experience even minor genomic variation, like Campylobacter, since the restriction fragment pattern can be altered (Fitzgerald et al, 2005)
Similar to pulse-field gel electrophoresis (PFGE), this method works well to discriminate between strains of genomically stable pathogens, but has limited efficacy when distinguishing between strains of Campylobacter due to inherent hypervariability of the genome (Parkhill et al, 2000)
Summary
As a leading cause of bacterial-derived gastroenteritis worldwide, Campylobacter species have a significant impact on human health (Kaakoush et al, 2015; Crofts et al, 2018) with approximately 96 million global cases (Kirk et al, 2015) and 1.3 million cases in the United States, annually (Fitzgerald et al, 2016). Pulse-field gel electrophoresis (PFGE) was highly impactful in identifying foodborne outbreaks and performing bacterial source-tracking of E. coli and Salmonella serotypes (Johnson et al, 1995; Fugett et al, 2007) Since this method relies on gel-based resolution of genomic restriction fragments, it can fail to discriminate between strains of bacterial species that experience even minor genomic variation, like Campylobacter, since the restriction fragment pattern can be altered (Fitzgerald et al, 2005). To circumvent these limitations, multi-locus sequence typing (MLST) was used by state and federal public health agencies to discriminate between strains and identify sources of infections for pathogens that were not amenable to PFGE. These changes were instituted due to several perceived advantages, including the ability to analyze bacterial genomes with single nucleotide-level resolution, regular access of more laboratories to sequencing technology, rapidly decreasing costs of sequencing a genome, and increased speed of sequencing (Salipante et al, 2015)
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