Local genes for local bacteria: evidence of allopatry in the genomes of transatlantic Campylobacter populations

The genetic structure of bacterial populations can be related to geographical locations of isolation. In some species, there is a strong correlation between geographical distance and genetic distance, which can be caused by different evolutionary mechanisms. Patterns of ancient admixture in Helicobacter pylori can be reconstructed in concordance with past human migration, whereas in Mycobacterium tuberculosis it is the lack of recombination that causes allopatric clusters. In Campylobacter, analyses of genomic data and molecular typing have been successful in determining the reservoir host species, but not geographical origin. We investigated biogeographical variation in highly recombining genes to determine the extent of clustering between genomes from geographically distinct Campylobacter populations. Whole genome sequences from 294 Campylobacter isolates from North America and the UK were analysed. Isolates from within the same country shared more recently recombined DNA than isolates from different countries. Using 15 UK/American closely matched pairs of isolates that shared ancestors, we identify regions that have frequently and recently recombined to test their correlation with geographical origin. The seven genes that demonstrated the greatest clustering by geography were used in an attribution model to infer geographical origin which was tested using a further 383 UK clinical isolates to detect signatures of recent foreign travel. Patient records indicated that in 46 cases travel abroad had occurred less than two weeks prior to sampling and genomic analysis identified that 34 (74%) of these isolates were of a non-UK origin. Identification of biogeographical markers in Campylobacter genomes will contribute to improved source attribution of clinical Campylobacter infection and inform intervention strategies to reduce campylobacteriosis

Association of insularity and body condition to cloacal bacteria prevalence in a small shorebird

Do islands harbour less diverse disease communities than mainland? The island biogeography theory predicts more diverse communities on mainland than on islands due to more niches, more diverse habitats and availability of greater range of hosts. We compared bacteria prevalences ofCampylobacter,ChlamydiaandSalmonellain cloacal samples of a small shorebird, the Kentish plover (Charadrius alexandrinus) between two island populations of Macaronesia and two mainland locations in the Iberian Peninsula. Bacteria were found in all populations but, contrary to the expectations, prevalences did not differ between islands and mainland. Females had higher prevalences than males forSalmonellaand when three bacteria genera were pooled together. Bacteria infection was unrelated to bird's body condition but females from mainland were heavier than males and birds from mainland were heavier than those from islands. Abiotic variables consistent throughout breeding sites, like high salinity that is known to inhibit bacteria growth, could explain the lack of differences in the bacteria prevalence between areas. We argue about the possible drivers and implications of sex differences in bacteria prevalence in Kentish plovers

Distribution and Genetic Profiles of Campylobacter in Commercial Broiler Production from Breeder to Slaughter in Thailand

Poultry and poultry products are commonly considered as the major vehicle of Campylobacter infection in humans worldwide. To reduce the number of human cases, the epidemiology of Campylobacter in poultry must be better understood. Therefore, the objective of the present study was to determine the distribution and genetic relatedness of Campylobacter in the Thai chicken production industry. During June to October 2012, entire broiler production processes (i.e., breeder flock, hatchery, broiler farm and slaughterhouse) of five broiler production chains were investigated chronologically. Representative isolates of C. jejuni from each production stage were characterized by flaA SVR sequencing and multilocus sequence typing (MLST). Amongst 311 selected isolates, 29 flaA SVR alleles and 17 sequence types (STs) were identified. The common clonal complexes (CCs) found in this study were CC-45, CC-353, CC-354 and CC-574. C. jejuni isolated from breeders were distantly related to those isolated from broilers and chicken carcasses, while C. jejuni isolates from the slaughterhouse environment and meat products were similar to those isolated from broiler flocks. Genotypic identification of C. jejuni in slaughterhouses indicated that broilers were the main source of Campylobacter contamination of chicken meat during processing. To effectively reduce Campylobacter in poultry meat products, control and prevention strategies should be aimed at both farm and slaughterhouse levels

Number of samples collected throughout chicken production process of 5 production chains.

<p>Number of samples collected throughout chicken production process of 5 production chains.</p

Types and number of samples collected throughout the chicken meat production chain.

<p>Area of boot swab sampling at downtime period included anteroom of the target house, inside the target house and area around the house. Area of boot swab sampling during the rearing period included path-leading to the house, anteroom of the target house, inside the target house, area around the house and inside the adjacent house. Flocks D and E were visited at 7^th, 14^th, 21^st, 28^th, 35^th day of the rearing period, while other flocks were visited at 7^th, 14^th, 17^th, 21^st, 24^th, 28^th, 31^st, 35^th, 38^th day of the rearing period.</p

Distribution and Genetic Profiles of <i>Campylobacter</i> in Commercial Broiler Production from Breeder to Slaughter in Thailand

<div><p>Poultry and poultry products are commonly considered as the major vehicle of <i>Campylobacter</i> infection in humans worldwide. To reduce the number of human cases, the epidemiology of <i>Campylobacter</i> in poultry must be better understood. Therefore, the objective of the present study was to determine the distribution and genetic relatedness of <i>Campylobacter</i> in the Thai chicken production industry. During June to October 2012, entire broiler production processes (i.e., breeder flock, hatchery, broiler farm and slaughterhouse) of five broiler production chains were investigated chronologically. Representative isolates of <i>C</i>. <i>jejuni</i> from each production stage were characterized by <i>flaA</i> SVR sequencing and multilocus sequence typing (MLST). Amongst 311 selected isolates, 29 <i>flaA</i> SVR alleles and 17 sequence types (STs) were identified. The common clonal complexes (CCs) found in this study were CC-45, CC-353, CC-354 and CC-574. <i>C</i>. <i>jejuni</i> isolated from breeders were distantly related to those isolated from broilers and chicken carcasses, while <i>C</i>. <i>jejuni</i> isolates from the slaughterhouse environment and meat products were similar to those isolated from broiler flocks. Genotypic identification of <i>C</i>. <i>jejuni</i> in slaughterhouses indicated that broilers were the main source of <i>Campylobacter</i> contamination of chicken meat during processing. To effectively reduce <i>Campylobacter</i> in poultry meat products, control and prevention strategies should be aimed at both farm and slaughterhouse levels.</p></div

<i>Campylobacter</i> genotypes detected in each chicken meat production units.

<p><i>Campylobacter</i> genotypes detected in each chicken meat production units.</p

Phylogenetic relationship of <i>Campylobacter jejuni</i> from various sources of broiler production processes.

<p>Distribution of sequence types in each production chain (i.e., A, B, C, D and E) and production unit (breeder farm, broiler farm and slaughterhouse) was represented by different shading pattern and geometric shape, respectively. Asterisk (*) defined as unassigned clonal complexes.</p