Exposure to poultry for cullers in the 12 months prior to serum sample collection.

<p>*chicken and/or ducks.</p

Serotype distribution across <i>Streptococcus suis</i> strains isolated from pig tonsils.

<p>@ Serotyping was repeated three times; additional analysis of 7 representative strains by MLST and 16S rDNA sequencing confirmed that these strains are S. suis.</p><p>*Includes serotype 5, 8, 9,10, 11, 12, 13, 15, 19, 20, 22, 23, 25, 26, 27, 28, 29, 30, 31, 33.</p><p>**Strains reacting with antisera against two or three different serotypes.</p><p>#23 strains were auto-agglutinating, 16 strains could not be assigned to any serotype after agglutination with polyvalent antisera, and 6 strains reacted negatively with all poly-valent antisera.</p

Protective measures taken by poultry workers and cullers during live poultry exposure as part of poultry work (poultry farmers) or culling (cullers).

<p>*138/183 poultry farmers and 240/317 cullers were exposed to live poultry during the 6 months prior to sample collection.</p

Exposure to poultry for poultry workers in the 12 months prior to serum sample collection.

<p>*Missing data for 8 poultry workers.</p><p>#Missing data for 2 poultry workers.</p

Sampling of tonsils and associated culture results.

<p>*Pigs sampled in slaughterhouse I originated from (number of samples): Ben Tre province (25), Binh Duong province (31), Dong Nai province (75); slaughterhouse II: Binh Duong province (55), Binh Thuan province (83), Ho Chi Minh City (Hoc Mon) (12), Long An province (30), Tien Giang province (34); slaughterhouse III: Binh Duong province (50), Ho Chi Minh City (Cu Chi) (84), Long An province (37).</p

Provinces of Vietnam.

<p>Provinces (coloured) from which sampled pig originated are located in the south of Vietnam and surrounding Ho Chi Minh City.</p

Pulse field gel electrophoresis (PFGE) of <i>Streptococcus suis</i> serotype 2 strains isolated from tonsils of healthy pigs.

<p>Six <i>S. suis</i> serotype 2 strains isolated from patients with meningitis in southern Vietnam whose PFGE patterns represent the dominant PFGE patterns across <i>S. suis</i> serotype 2 strains isolated from humans (labeled A–F), were included for comparison purpose. A dendrogram was generated by Dice analysis (band tolerance, 1.3%) and cluster analysis with unweighted pair group method with arithmetic mean, using Bionumerics software (Applied Maths, Belgium). Bars indicate 95% confidence intervals. Columns: Cls: PFGE cluster; Pro: province of pig's origin or patients' residence; Date: date of tonsil collection or patients' admission; SH: slaughterhouse ID; WS: Whole sale seller ID; ST: sequence type, Res: tetracycline and erythromycin resistance gene detected by PCR and sequencing, ef: <i>epf</i> or <i>epf*</i> gene detected by PCR. CC: Cu Chi- HCMC; LA: Long An; HM: Hoc Mon – HCMC; HCM: Ho Chi Minh City; BD: Binh Duong; BTr: Ben Tre; DN: Dong Nai; BTh: Binh Thuan. O: amplicons of <i>tet</i>(O) gene detected. M: amplicons of <i>tet</i>(M) gene detected. B: amplicons of <i>erm</i>(B) gene detected. L: amplicons of <i>tet</i>(L) gene detected *: amplicons of mosaic tetracyclin resistance encoding gene <i>tet</i>(O/W/32/O) detected in these strains. #: no amplicons of <i>erm</i>(A), <i>erm</i>(B) or <i>mef</i>(A) were detected in these erythormycine resistant strains. 0: no amplicons of <i>epf</i> or <i>epf*</i> gene detected. 1: amplicons of <i>epf</i> gene detected. 2: amplicons of <i>epf</i>* gene detected.</p

Kobuvirus time-scaled tree mapping with host traits

Maximum Clade Credibility (MCC) tree representing the time-scale phylogeny of kobuvirus from all hosts based on the VP1 gene (n=416). Tree was genereated using Beast V1.8.2.The best fitting model was a general time-reversible (GTR) model with a gamma distribution (G) across sites as the substitution model, with an uncorrelated log-normal relaxed molecular clock model and with a constant size coalescent process prior over the phylogenies. The MCMC chains were run for 100 million iterations with sub-sampling every 10,000 iterations and 10% burn-in.we applied a strong prior of substitution rate using a normal distribution (mean rate = 2×10-3 substitutions/site/year; Standard Deviation =5×10-4).An asymmetric model with Bayesian Stochastic Search Variable selection (BSSVS) was applied to identify statistically significant transition rates between host species and geographic locations.The tree file was viewed and edited in Figtree V1.4.2