Understanding the genetic architecture of economically important traits is essential for the design and implementation of efficient breeding programs. Here, we analysed 3,653 Eastern oysters (Crassostrea virginica) from 62 crossing groups and 307 full-sib families, all genotyped with a 200 K SNP array, to (i) estimate heritability and genetic correlations for six growth-related traits, (ii) detect quantitative trait loci (QTL) and candidate genes, and (iii) compare the accuracy of pedigree- (PBLUP) versus genomic-based (GBLUP) predictions across marker densities, selection strategies (physical distance (PD) versus linkage disequilibrium (LD) and phenotype-based genotyping strategies. SNP-based Heritabilities ranged from 0.33 to 0.56, and genetic correlations among traits exceeded 0.61, indicating strong pleiotropy. GWAS revealed a polygenic architecture with a shared QTL on chromosome 2; the top SNP explained ≤ 1.1% of phenotypic variance. Except for the 0.5 K LD panel—where PBLUP was more accurate—and the 1 K LD panel—where both methods performed similarly—GBLUP outperformed PBLUP in all scenarios, with the greatest advantage observed for physically spaced (PD) panels. The highest accuracy (0.80) was achieved with the full 100 K SNP set. GBLUP models required panels containing ≥ 0.5 K PD (accuracy ≥ 0.55) or ≥ 2 K LD (accuracy ≥ 0.56) to significatively surpass PBLUP predictions. Training sets built from extreme phenotypes boosted accuracy in small to intermediate sample sizes (e.g., 0.74 at n = 1,500 with 5 K PD SNPs versus 0.53 under random sampling). These results provide novel insights into not only the genomic regions controlling growth in this species but also about the utility of PD-based SNP panels and balanced sampling designs for enhancing GS accuracy in C. virginica.

Antimicrobial resistance (AMR) is a significant global challenge that affects environmental, animal, and human health, with reports of antimicrobial-resistant bacteria and antimicrobial resistance genes becoming increasingly common across these domains. This study aimed to systematically review and compare the occurrence of AMR in bacterial isolates from wild animals in South America, focusing on environments with varying levels of anthropogenic impact. Half of the countries in South America documented AMR in wild animals at least once. Most studies focused on specific animal classes, particularly Aves and Mammalia, with a notable emphasis on the orders Chiroptera and Rodentia, as well as the bacterial species Escherichia coli and Salmonella enterica. Subgroup meta-analyses revealed that, for most antimicrobials, the proportion of AMR was significantly higher in environments with a high anthropogenic impact compared to those with a low anthropogenic impact. However, there were no significant differences between the two types of environments for some antimicrobials. Interestingly, certain beta-lactams showed a higher proportion of AMR in environments with low anthropogenic impact. These findings raise important questions regarding the origins and spread of AMR in wild animals, underscoring the necessity for further research to understand the dynamics of AMR in areas with varying levels of human intervention.

In the Metropolitana region of Chile there are 3836 backyard production systems (BPS), characterized as small-scale systems. They act as a source of zoonotic pathogens, such as Salmonella enterica and Shiga toxin-producing Escherichia coli (STEC), whose prevalence in BPS has not been fully described. The objective of this study was to determine the positivity for both agents in BPS and to establish the risk factors related to their presence. In each BPS, an epidemiological survey was undertaken, and stool samples were collected to detect these pathogens via bacteriological culture and conventional PCR techniques. Subsequently, multivariable logistic regression models were applied to establish the risk factors associated with their presence. BPS positivity rates of 11.76% for STEC and 4.7% for S. enterica were observed. The systems showed poor welfare standards and a lack of biosecurity measures. The risk factor analysis concluded that the Gini–Simpson index (p = 0.030; OR = 1.717) and the presence of neighboring intensive poultry or swine production systems (p = 0.019; OR = 20.645) act as factors that increased the risk of positivity with respect to STEC. In the case of S. enterica, exchanging embryonated eggs (p = 0.021; OR = 39) and the presence of debeaked chickens (p = 0.001; OR = 156) were determined as factors that increased the risk of positivity for this agent. For positivity with respect to both pathogens, the Gini–Simpson index (p = 0.030; OR = 1.544) and being INDAP/PRODESAL users (p = 0.023; OR = 15.026) were determined as factors that increased the risk, whereas the type of confinement (p = 0.002; OR = 0.019) decreased it. Epidemiological surveillance of these neglected populations is lacking, highlighting the fact that STEC and S. enterica maintenance on BPS represents a potential threat to public health.

Backyard production systems (BPS) are distributed worldwide, rearing animals recognized as reservoirs of Salmonella enterica and Shiga toxin-producing Escherichia coli (STEC), both zoonotic pathogens. The aim of this study was to characterize isolates of both pathogens obtained from animals raised in BPS from two central Chile regions. The presence of pathogens was determined by bacterial culture and confirmatory PCR for each sampled BPS, calculating positivity rates. Multivariate logistic regression was used to determine risk factors. Additionally, phenotypic antimicrobial resistance was determined. A positivity rate of 2.88% for S. enterica and 14.39% for STEC was determined for the complete study region (Valparaíso and Metropolitana regions). Risk factor analysis suggests that the presence of ruminants (OR = 1.03; 95% CI = 1.002–1.075) increases the risk of STEC-positive BPS, and the presence of ruminants (OR = 1.05; 95% CI = 1.002–1.075) and the animal handlers being exclusively women (OR = 3.54; 95% CI = 1.029–12.193) increase the risk for S. enterica/STEC positivity. Eighty percent of S. enterica isolates were multidrug resistant, and all STEC were resistant to Cephalexin. This study evidences the circulation of multidrug-resistant zoonotic bacterial strains in animals kept in BPS and the presence of factors that modify the risk of BPS positivity for both pathogens.