Data_Sheet_1_Population Structure, Antimicrobial Resistance, and Virulence-Associated Genes in Campylobacter jejuni Isolated From Three Ecological Niches: Gastroenteritis Patients, Broilers, and Wild Birds.PDF

<p>Campylobacter jejuni is the causal agent of the food-borne infection with the highest incidence in Europe. Both poultry and wild birds are a major reservoir. To gain insight into the population structure, virulence potential, and antimicrobial resistance (AMR), a collection of 150 isolates from three different ecological niches (broilers, wild birds, and human patients) was studied. Despite the high genetic diversity found, the population structure defined two distinct clusters, one formed mostly by broiler and human isolates and another one by most wild bird isolates. The ST-21 complex exhibits highest prevalence (in humans and broilers), followed by ST-1275 complex (only in wild birds). The ST-48, -45, and -354 complexes were found in all three niches, but represent only 22 out of 150 studied strains. A higher occurrence of AMR and multidrug resistance was detected among broiler and human isolates. Moreover, significant differences were found in the distribution of certain putative virulence genes. Remarkably, many wild bird strains were negative for either cdtA, cdtB, or cdtC from the canonical strain 81-176, whereas all broiler and human strains were positive. These data suggest that the different variants of the cdt genes might be relevant for the efficient colonization of certain hosts by C. jejuni. Our study contributes to the understanding of the role of the diverse Campylobacter reservoirs in the transmission of campylobacteriosis to humans.</p

Additional file 1: Figure S1. of NKX2–1 expression as a prognostic marker in early-stage non-small-cell lung cancer

NKX2–1 expression according to TTF-1 immunohistochemistry. Figure S2. Kaplan Meier analysis of disease-free survival according to NKX2–1 expression levels in (A) the entire cohort and (B) patients with stage I disease. Figure S3. Kaplan Meier analysis of overall survival according to miR-365 expression levels in (A) the entire cohort and (B) patients harboring neither TP53 nor KRAS mutations. Figure S4. Kaplan Meier analysis of overall survival according to NKX2–1 expression levels in (A) patients with wild-type TP53, (B) patients with TP53 mutations, (C) patients with wild-type KRAS, and (D) patients with KRAS mutations. Figure S5. Kaplan Meier analysis of the impact of NKX2–1 in overall survival in stage I disease (A) WT TP53 patients, (B) TP53 mutated patients, (C) KRAS WT patients, and (D) KRAS mutated patients. (PDF 276 kb

<i>Trypanosoma cruzi</i> diagnostic Real-Time PCR results obtained in the eight protocols assessed for the 22 discordant samples.

<p><i>Trypanosoma cruzi</i> diagnostic Real-Time PCR results obtained in the eight protocols assessed for the 22 discordant samples.</p

Degree of agreement between protocols A and H based on a Bland-Altman plot of the nine samples with quantifiable results in both methods.

<p>Each sample is represented by plotting the mean of the measurements obtained in protocols A and H on the x-axis and the difference of the same two values on the y-axis. SD: standard deviation. Log₁₀ par. eq./10 mL: logarithmic values of parasite equivalents in 10 mL of blood.</p

<i>Trypanosoma cruzi</i> diagnostic Real-Time PCR results of samples analysed according to the protocols used in the study based on the combination of different sample treatments, DNA extraction methods and Real-Time PCR procedures.

<p><i>Trypanosoma cruzi</i> diagnostic Real-Time PCR results of samples analysed according to the protocols used in the study based on the combination of different sample treatments, DNA extraction methods and Real-Time PCR procedures.</p

Cohen’s kappa coefficient (K) results for the comparison between protocols with the sample treatment as the only variable.

<p>K values are shown including and excluding inhibited samples.</p