Antibiotics are used in animal husbandry to control infectious diseases. Different stressors can compromise animal health, leaving piglets vulnerable to pathogens, especially enterotoxigenic Escherichia coli (ETEC), which causes post-weaning diarrhoea (PWD), the major source of mortality and morbidity in swine production. Furthermore, PWD is a recurrent disease for certain farms, suggesting a link between gut microbial composition and animal health. The aim of this study was to identify the intestinal microbiota of pigs on farms with high health status (HHS) and low health status (LHS) to determine the relationships between sanitary status and gut health. Therefore, three pig farms with LHS presenting recurrent problems of PWD and three farms with HHS were selected to characterise the intestinal microbiome of sows and their piglets. 16 S rRNA gene sequencing technology was used to determine the associations of the gut microbiome with health. With the aim of bringing the MinION Nanopore device to the field for its portability and taxonomic resolution, the results obtained with Illumina were compared to those obtained with Nanopore. Overall, the results indicated remarkable differences in intestinal microbial communities between animals from LHS farms and those from HHS farms, suggesting that the microbiomes of LHS animals were enriched with potential pathogenic microorganisms, mainly from the Pseudomonadota phylum, such as the genus Escherichia-Shigella, and their associated related species. Moreover, animals from HHS were enriched with beneficial microorganisms, such as Lactobacillus spp., Christensenellaceae R7 group, Treponema, Acetitomaculum and Oscillospiraceae UCG-005. This study identifies potential microorganisms that may contribute to health and disease in pig farms with HHS and LHS, suggesting that tracking their occurrence might provide insight into sanitary conditions. Moreover, this research highlights the compatibility between Illumina and Nanopore sequencing platforms, justifying the use of MinION Nanopore device in field applications for in situ studies of PWD. This application has the potential to enhance sustainable economic growth in swine farms by enabling more effective monitoring and management of animal health.

Antimicrobial resistance poses a major threat to global health and food security and is primarily driven by antimicrobial use in human and veterinary medicine. Understanding its epidemiology at farm level is crucial for effective control measures. Despite the significant reduction in antibiotic use in conventional livestock production, the swine sector traditionally has a higher level of antibiotic use in veterinary medicine. Consequently, multidrug resistance (MDR) among microbial isolates of swine origin has been relatively frequent. The aim of this study was to assess the presence of multidrug-resistant (MDR) bacteria, enteric pathogens and resistance genes to the main antibiotics used in clinical practice, both within the environment and in animals across pig farms characterized by varying degrees of sanitary status. A total of 274 samples were collected. Of these, 34 samples were collected from the environment (wall swabs, slat swabs and slurry pit), and 240 samples were collected from animals (sows’ and piglets’ rectal faeces). All samples were analysed for MDR bacteria and enteric pathogens. The study revealed a high frequency of extended-spectrum beta-lactamases (ESBL)-producing Enterobacterales and Campylobacter spp., with ESBL-producing Enterobacterales predominating in high health status farms (environment and animals) and Campylobacter spp. in both high health status and low health status environments. Additionally, a high percentage of methicillin-resistant Staphylococcus aureus (MRSA) was found, mainly in environmental samples from high health status farms, and Clostridioides difficile was distributed ubiquitously among farms and samples. Furthermore, though less frequently, vancomycin-resistant Enterococcus faecium (VRE) was isolated only in high health status farms, and Gram-negative bacilli resistant to carbapenems were isolated only in environmental samples of high health status and low health status farms. This study underscores the importance of surveillance for MDR bacteria in farm animals and their environment, including their waste. Such ecosystems serve as crucial reservoirs of bacteria, requiring national-level surveillance to promote responsible antibiotic use and pandemic control.

Background/Aims : The presence of pathogens such as Salmonella enterica and Escherichia coli in infant formulas, even at concentrations below the detection threshold, poses a health risk. Probiotics have been proposed as a strategy to limit pathogen proliferation. This study evaluated two probiotic strains (Lacticaseibacillus rhamnosus HN001 and Bifidobacterium longum subsp. infantis IM-1) to inhibit the growth of these pathogens under simulated conditions. Methods: Assays were conducted using reconstituted infant formula supplemented or not with the probiotics combination and challenged with E. coli or Salmonella enterica at low inoculum levels (1 or 10 CFU/10 g). A total of 112 samples were analyzed across eight trials, with two time points (T0h and T18h). Microbial composition was characterized by sequencing the V4 region of the 16S rRNA gene followed by bioinformatic analysis using QIIME2 and the SILVA database. Results: In the absence of probiotics, E. coli and Salmonella enterica showed a marked increase in relative abundance under the tested conditions (samples C1 and C10), reaching high relative abundances at T18h. In contrast, formulas supplemented with Bifidobacterium longum subsp. infantis IM-1 and Lacticaseibacillus rhamnosus HN001 were associated with markedly lower pathogen relative abundances of both pathogens, which were either undetectable or reduced to <1% in most conditions. A concurrent increase in beneficial bacterial genera such as Lacticaseibacillus and Lactobacillus was observed, indicating competition for ecological niches and nutrients. Conclusions: The probiotics Bifidobacterium longum subsp. infantis IM-1 and Lacticaseibacillus rhamnosus HN001 exerted a reduced proliferation effect against E. coli and Salmonella enterica in infant formulas contaminated at low inoculum levels, limiting pathogen proliferation and promoting the stability of beneficial microbiota. These findings suggest that incorporating probiotics may limit pathogen proliferation in infant formulas under the experimental conditions evaluated.