Whole genome sequencing of Shigella sonnei through PulseNet Latin America and Caribbean: advancing global surveillance of foodborne illnesses

Objectives Shigella sonnei is a globally important diarrhoeal pathogen tracked through the surveillance network PulseNet Latin America and Caribbean (PNLA&C), which participates in PulseNet International. PNLA&C laboratories use common molecular techniques to track pathogens causing foodborne illness. We aimed to demonstrate the possibility and advantages of transitioning to whole genome sequencing (WGS) for surveillance within existing networks across a continent where S. sonnei is endemic. Methods We applied WGS to representative archive isolates of S. sonnei (n = 323) from laboratories in nine PNLA&C countries to generate a regional phylogenomic reference for S. sonnei and put this in the global context. We used this reference to contextualise 16 S. sonnei from three Argentinian outbreaks, using locally generated sequence data. Assembled genome sequences were used to predict antimicrobial resistance (AMR) phenotypes and identify AMR determinants. Results S. sonnei isolates clustered in five Latin American sublineages in the global phylogeny, with many (46%, 149 of 323) belonging to previously undescribed sublineages. Predicted multidrug resistance was common (77%, 249 of 323), and clinically relevant differences in AMR were found among sublineages. The regional overview showed that Argentinian outbreak isolates belonged to distinct sublineages and had different epidemiologic origins. Conclusions Latin America contains novel genetic diversity of S. sonnei that is relevant on a global scale and commonly exhibits multidrug resistance. Retrospective passive surveillance with WGS has utility for informing treatment, identifying regionally epidemic sublineages and providing a framework for interpretation of prospective, locally sequenced outbreaks

New insights into the genetic etiology of Alzheimer's disease and related dementias

Characterization of the genetic landscape of Alzheimer's disease (AD) and related dementias (ADD) provides a unique opportunity for a better understanding of the associated pathophysiological processes. We performed a two-stage genome-wide association study totaling 111,326 clinically diagnosed/'proxy' AD cases and 677,663 controls. We found 75 risk loci, of which 42 were new at the time of analysis. Pathway enrichment analyses confirmed the involvement of amyloid/tau pathways and highlighted microglia implication. Gene prioritization in the new loci identified 31 genes that were suggestive of new genetically associated processes, including the tumor necrosis factor alpha pathway through the linear ubiquitin chain assembly complex. We also built a new genetic risk score associated with the risk of future AD/dementia or progression from mild cognitive impairment to AD/dementia. The improvement in prediction led to a 1.6- to 1.9-fold increase in AD risk from the lowest to the highest decile, in addition to effects of age and the APOE ε4 allele

Evaluation of producing and marketing entire male pigs

This paper presents the results of a research program that was aimed at evaluating: (1) sensory evaluation of meat from entire male pigs, (2) preventive measures to reduce boar taint prevalence, (3) accuracy of detection for boar taint, and (4) the relationship between farm management characteristics and levels of mounting and aggressive behaviour of boars. Using observational and experimental studies data were collected in various segments of the pork supply chain. Consumer acceptance of meat from entire male pigs was evaluated. The effectiveness of preventive measures to reduce boar taint prevalence was determined. The relationship of farm (management) characteristics with boar taint prevalence, animal behaviour, skin lesions and lameness respectively was analysed. The similarity of the rank order between consumer perception of odour and human nose scores, skatole and androstenone levels respectively was determined. Consumers evaluate meat that passed the boar taint detection test comparable to meat from gilts. Meat samples that did not pass this test were evaluated less favourable. Ranking AI boars on their genomic breeding values for low boar taint resulted in a reduction in boar taint prevalence of 40%. The skatole level is lower in boars fed via a long trough than in boars fed by a single space feeder. Few eating places, restricted feeding, a low level of amino acids in the diet, insufficient water supply of the drinking system, illness of the pigs, a suboptimal climate and fear for humans were associated with a higher level of sexual and aggressive behaviour and more skin lesions. A partly open pen wall, clean pens and pigs, wider gaps of the slats, feeding by a long trough, and feeding wet by-products were associated with less sexual and aggressive behaviour and less skin lesions. Having more than 30 animals per pen was associated with a higher probability of high boar taint prevalence levels. Hygienic conditions were associated with lower boar taint prevalence levels. Assessing similarity of the rank order comparison between consumer perception and three selected boar taint detection parameters for the consumer perception attribute odour of meat resulted in the highest Kendall's W values for the human nose scores. In conclusion, boar tainted meat was rated as less pleasant by consumers compared to meat of gilts and non-tainted boar meat, indicating the need of detection as a safety net at the slaughter line. Breeding was an effective preventive measure to reduce boar taint. Farms with appropriate management, feeding and housing conditions have reduced levels of mounting and aggressive behaviour. Human nose scores were a better predictor of the rank order of consumer perception, compared to skatole levels and to androstenone levels