Number of farms during the five study years grouped by the frequency of <i>C</i>. <i>jejuni</i> positive chicken batches delivered to slaughter annually (data on farms which delivered no positive batches has been omitted).

<p>In <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0116585#pone.0116585.g001" target="_blank">Fig. 1A</a>) the numbers are counted on the basis of all 380 <i>C</i>. <i>jejuni</i> isolates acquired in the study, whereas in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0116585#pone.0116585.g001" target="_blank">Fig. 1B</a>) the numbers are based on the adjusted database. In the latter database, isolates with similar MLST and PFGE types collected within a week of each other and originating from the same farm was counted as one clone to account for clustering of flocks within the farms.</p

Percentages of resistant <i>E</i>. <i>coli</i> isolates (N = 111) from faeces of weaned pigs isolated on MacConkey plates with and without 10 mg/l ampicillin (AMP).

<p>Percentages of resistant <i>E</i>. <i>coli</i> isolates (N = 111) from faeces of weaned pigs isolated on MacConkey plates with and without 10 mg/l ampicillin (AMP).</p

Effects of amoxicillin (ANT) or no (CON) treatment for newborn piglets on occurrence ratio and the size of hernias, abscesses or both in umbilical and inguinal areas at nine weeks of age ¹.

<p>Effects of amoxicillin (ANT) or no (CON) treatment for newborn piglets on occurrence ratio and the size of hernias, abscesses or both in umbilical and inguinal areas at nine weeks of age <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0172150#t001fn001" target="_blank">¹</a>.</p

The occurrence ratio of piglets treated for different diseases during the suckling period after routine amoxicillin injection during the first day of life (ANT) or no treatment (CON).¹

<p>The occurrence ratio of piglets treated for different diseases during the suckling period after routine amoxicillin injection during the first day of life (ANT) or no treatment (CON).<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0172150#t002fn001" target="_blank">¹</a></p

Body weight of 820 pigs with no palpable defects in umbilical or inguinal area at four and nine weeks of age.

<p>The pigs were treated with a single amoxicillin injection one day after birth (ANT, N = 405), or not treated (CON, N = 415). Asterisks (***) indicate that variables were significantly different (<i>P</i> < 0.0001).</p

Resistance profiles of <i>E</i>. <i>coli</i> isolated on MacConkey with and without 10 mg/l ampicillin (AMP) and their counts.

<p>Resistance profiles of <i>E</i>. <i>coli</i> isolated on MacConkey with and without 10 mg/l ampicillin (AMP) and their counts.</p

Body weight of pigs with umbilical hernia (UH), umbilical abscess (UA), umbilical hernia + abscess (UHA), inguinal hernia (IH), inguinal abscess (IA), inguinal hernia + abscess (IHA), or with no defects (ND).

<p>The numbers in the figure represent the number of affected pigs (four weeks/nine weeks). Different letters (a, b) indicate that there were significant differences between variables (<i>P</i> < 0.05).</p

Phylogeography of the widespread Campylobacter jejuni ST45 clonal complex using whole genome sequencing

<p>Identifying spatiotemporal genetic changes in the pathogen populations circulating in a given area is critical for forecasting the epidemiological relationship between isolates. In Finland, C. jejuni ST-45cc is the most abundant genotype among the domestically acquired human infections, and almost half of the chicken flocks are positive. However, little is known on the population stability over time and space. Thus, to explore spatiotemporal patterns of genetic diversity within ST-45cc, we performed phylogenomic and genome-wide association studies (GWAS) on 141 Finnish and 199 British isolates obtained during 14 years.</p> <p>Genealogy was reconstructed using maximum likelihood phylogenetic analysis of 1,043 core genes after deleting recombination regions using BRATNEXGEN. Population structure was inferred with BAPS. GWAS was facilitated by first running a distributed string mining method on both core and accessory genomic elements, and then testing for association among the resulting genetic features. RAxML and goeBURST were used to cluster strains based on distribution of 1,281 accessory genes. BEAST 1.8 was used for infering TMRCA on unrecombined core or shared genome. Genome Profiler was used to extract pangenome allele profile from monomorphic BAPS group 6.</p

wgMLST of <i>C</i>. <i>upsaliensis</i> isolates.

<p>SplitsTree of the NeighborNet network (664 shared genes) of all available <i>C</i>. <i>upsaliensis</i> whole genomes, including three reference strains and isolates from dogs that were sampled only once and thus not included in this study, using GeP (Zhang et al., 2015). A new GeP analysis was performed for all closely related isolates and the results are shown next to the pair of isolates. The number of allelic differences, observed in the primary GeP analysis among the 664 shared genes, are shown in parenthesis. The reference genomes DSM 5365, JV21 and RM3195 were obtained from GenBank (accession numbers JHZN00000000, NZ_AEPU00000000 and NZ_AAFJ00000000).</p

ClonalFrame genealogy tree based on all known <i>C</i>. <i>upsaliensis</i> MLST allele sequences.

<p>Novel STs reported in this study are indicated in bold. The sources of the isolates are indicated based on the information available in the PubMLST <i>Campylobacter</i> non <i>jejuni/coli</i> database and in Parsons et al. (2012).</p