We show that a higher incidence of campylobacteriosis is found in young children (age, <5 years) living in rural, compared with urban, areas. Association of this difference with particular animal sources was evaluated using multilocus sequence typing. This evaluation was achieved by comparing Campylobacter isolates originating from these children, retail poultry, and a range of animal sources by use of source attribution and phylogenetic analysis methods. The results indicate that chicken is a major source of infection in young urban children, although not in their rural counterparts, for which ruminant and other avian sources are more important.

The common zoonotic pathogen Campylobacter coli is an important cause of bacterial gastroenteritis worldwide but its evolution is incompletely understood. Using multilocus sequence type (MLST) data of 7 housekeeping genes from a national survey of Campylobacter in Scotland (2005/6), and a combined population genetic-phylogenetics approach, we investigated the evolutionary history of C. coli. Genealogical reconstruction of isolates from clinical infection, farm animals and the environment, revealed a three-clade genetic structure. The majority of farm animal, and all disease causing genotypes belonged to a single clade (clade 1) which had comparatively low synonymous sequence diversity, little deep branching genetic structure, and a higher number of shared alleles providing evidence of recent clonal decent. Calibration of the rate of molecular evolution, based on within-species genetic variation, estimated a more rapid rate of evolution than in traditional estimates. This placed the divergence of the clades at less than 2500 years ago, consistent with the introduction of an agricultural niche having had an effect upon the evolution of the C. coli clades. Attribution of clinical isolate genotypes to source, using an asymmetric island model, confirmed that strains from chicken and ruminants, and not pigs or turkeys, are the principal source of human C. coli infection. Taken together these analyses are consistent with an evolutionary scenario describing the emergence of agriculture-associated C. coli lineage that is an important human pathogen.

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This report presents the results of the project "Closing gaps for performing a risk assessment on Listeria monocytogenes in ready-to-eat (RTE) foods: activity 3, the comparison of isolates from different compartments along the food chain, and from humans using whole genome sequencing (WGS) analysis". The main objective was to compare L. monocytogenes isolates collected in the EU from ready-to-eat (RTE) foods, compartments along the food chain and from human cases by the use of WGS. A total of 1,143 L. monocytogenes isolates were selected for the study, including 333 human clinical isolates and 810 isolates from the food chain. The isolates were whole genome sequenced. The phylogeny showed a clear delineation between L. monocytogenes lineages and between clonal complexes within lineages. A range of typing methods were applied to the sequence data, providing the framework to answer questions on genetic diversity and epidemiological relationships. Retrospective analysis of nine outbreaks showed that WGS is a powerful tool in national and international outbreak investigations as WGS can accurately rule isolates in or out of outbreaks. Source attribution models showed bovine reservoir to be the main source of human disease although other sources also contributed and generally confidence intervals were high. Numerous consistent genetic linkages between a priori unlinked strains were identified, some of which involved isolates from multiple countries. The presence of putative markers conferring the potential to survive/multiply in the food chain and/or cause disease in humans was explored by detecting the presence of putative virulence genes, AMR genes and factors conferring the ability to persist in the food processing chain. This study has demonstrated one of the major benefits of WGS, which is the ability to address a wide range of questions including those on virulence, antimicrobial resistance, source attribution, surveillance and outbreak detection and investigation, in a single experiment.

We present the LiSEQ (Listeria SEQuencing) project, funded by the European Food Safety Agency (EFSA) to compare Listeria monocytogenes isolates collected in the European Union from ready-to-eat foods, compartments along the food chain (e.g. food-producing animals, food-processing environments) and humans. In this article, we report the molecular characterization of a selection of this data set employing whole-genome sequencing analysis. We present an overview of the strain diversity observed in different sampled sources, and characterize the isolates based on their virulence and resistance profile. We integrate into our analysis the global L. monocytogenes genome collection described by Moura and colleagues in 2016 to assess the representativeness of the LiSEQ collection in the context of known L. monocytogenes strain diversity.

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An intensive study of 443 isolates of Campylobacter jejuni and Campylobacter coli from 2031 fecal samples excreted by animal sources including cattle, sheep, and pigs, a range of wild and domesticated avian species and pets is described. The prevalence found in the majority of animal sources ranged from 22% to 28% with poultry being highest at 41% and cats and dogs lowest (<5%). The average count excreted for each animal source was found not to be significantly different ranging from approximately 10 2 to 10 5 cfu/g. Multilocus sequence typing (MLST) identified phylogenies that exhibited host specificity. A number of clonal complexes (CCs) and sequence types (STs) were characteristic of particular hosts (e.g., CC-179, ST-637, and ST-1341 found only in pigeons and gulls). Analysis of genetic distance demonstrated numerous significant differences in the distribution of MLST types (CC, ST, and allele) between animal sources. Host association was quantified using structure that correctly assigned the nine animal sources with accuracies of 28%, 24%, and 55% at the CC, ST, and allele levels, respectively. This is substantially higher than would be expected by random allocation (11%) but farmyard poultry had the lowest assignment accuracy (13%, 13%, and 21%) suggesting that isolates were shared with a wide range of other animals. This study demonstrates the link between MLST type and host and provides data that can be used in risk assessment and food attribution models. Further, it demonstrates the applicability of MLST to characterize Campylobacter strains from a broad range of environmental sources.

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