Integrated multi trophic aquaculture (IMTA) improves the production of aquatic animals by promoting nutrient utilization through different tropical levels. Microorganisms play an important role in elements cycling, energy flow and farmed-species health. The aim of this study was to evaluate how feed types, fresh frozen fish diet (FFD) or formulated diet (FD), influence the microbial community diversity and functionality in both water and sediment in a marine IMTA system. Preferable water quality, higher animal yields and higher cost efficiency were achieved in the FD pond. Feed types changed the pond bacterial community distribution, especially in the rearing water. The FFD pond was dominated with Cyanobacteria in the water, which played an important role in nitrogen fixation through photosynthesis due to the high nitrogen input of the frozen fish diet. The high carbohydrate composition in the formulated diet triggered higher metabolic pathways related to carbon and lipid metabolism in the water of the FD pond. Sediment had significantly higher microbial diversity than the rearing water. In sediment, the dominating genus, Sulfurovum and Desulfobulbus, were found to be positively correlated by network analysis, which had similar functionality in sulfur transformation. The relatively higher rates of antibiotic biosynthesis in the FFD sediment might be related to the pathogenic bacteria introduced by the trash fish diet. The difference in microbial community composition and metabolic pathways may be associated with the different pathways for nutrient cycling and animal growth performance. The formulated diet was determined to be more ecologically and economically sustainable than the frozen fish diet for marine IMTA pond systems.

Dairy cows are negatively affected by the introduction of bovine viral diarrhea virus (BVDV), and consequently, produce less milk. Existing literature on potential milk production losses is based on relatively outdated data and hardly evaluates milk production loss in relation to a new BVDV infection in a surveillance system. This study determined the annual and quarterly loss in milk production of BVDV introduction in 3,126 dairy herds participating in the Dutch BVDV-free program between 2007 and 2017. Among these herds, 640 were "breakdown-herds" that obtained and subsequently lost their BVDV-free status during the study period, and 2,486 herds obtained and retained their BVDV-free status during the study period. Milk yields before and after BVDV introduction were compared through annual and quarterly linear mixed models. The fixed variables for both models included herd type (breakdown-herd or free-herd), bovine viral diarrhea status (on an annual and quarterly basis), year, season, and a random herd effect. The dependent variable was the average daily milk yield on the test day. To define the possible BVDV-introduction dates, 4 scenarios were developed. In the default scenario, the date of breakdown (i.e., loss of the BVDV-free status) was assumed as the BVDV-introduction date. For the other 3 scenarios, the BVDV-introduction dates were set at 4, 6, and 9 mo before the date of breakdown, based on the estimated birth date of a persistently infected calf. In the default scenario, the loss in milk yield due to BVDV introduction occurred mainly in the first year after breakdown, with a reduction in yield of 0.08 kg/cow per day compared with the last year before breakdown. For the other 3 scenarios, the greatest yield reduction occurred in the second year after BVDV introduction, with a loss of 0.09, 0.09, and 0.1 kg/cow per day, respectively. For the first 4 quarters after BVDV introduction in the default scenario, milk yield loss was 0.14, 0.09, 0.02, and 0.08 kg/cow per day, respectively. These quarterly results indicated that milk yield loss was greatest in the first quarter after BVDV introduction. Overall, BVDV introduction had a negative, but on average a relatively small, effect on milk yield for herds participating in the BVDV-free program. This study will enable dairy farmers and policymakers to have a clearer understanding of the quantitative milk production effect of BVDV on dairy farms in a control program.

Specimens collected from dead pigs are a welfare-friendly and cost-effective active surveillance. This study aimed to evaluate the accuracy of different postmortem specimens from dead piglets for disease detection, using PRRSV as an example. Three farrow-to-wean farms undergoing PRRSV elimination were conveniently selected. Samples were collected at approximately 8- and 20-weeks post-outbreak. Postmortem specimens included nasal (NS), oral (OS), and rectal (RS) swabs, tongue-tip fluids (TTF), superficial inguinal lymph nodes (SIL), and intracardiac blood. These were tested individually for PRRSV by RT-PCR. Sensitivity, specificity, negative and positive predictive values, and agreement of postmortem specimens were calculated using intracardiac sera as the gold standard. OS and SIL had the best overall performance, with sensitivities of 94.6–100%, specificities of 83.9–85.1%, and negative predictive values of 97.3–100%. TTF had high sensitivity (92.2%) but low specificity (53.9%) and positive predictive value (48.3%). While challenges in meeting sampling targets due to variable pre-weaning mortality were noted, PRRS was detected in all postmortem specimens. OS and NS showed promising results for disease monitoring, though TTF, despite their sensitivity, had lower specificity, making them less suitable for individual infection assessment but useful for assessing environmental contamination.

Porcine Epidemic Diarrhea Virus (PEDV) was introduced in the United States (U.S.) in 2013, spreading rapidly and leading to economic losses. Two strains, S-INDEL and non-S-INDEL, are present in the U.S. We analyzed 313 genomes and 556 Spike protein sequences generated since its introduction. PEDV case numbers were highest during the first two years after its introduction (epidemic phase), then declined and stabilized in the following years (endemic phase). Sequence surveillance was higher during the initial epidemic phase. Our results suggest the non-S-INDEL strain is the predominant strain in U.S. The non-S-INDEL sequences exhibit pairwise nucleotide identity percentages above 97.6%. Most non-S-INDEL sequences sampled after 2017 clustered into two sub-clades. No descendants derived from other clades present in the epidemic period were detected in the contemporary data, suggesting that these clades are no longer circulating in the U.S. The two clades currently circulating are restricted to two respective geographic regions and our results suggest limited inter-regional spread. This insight helps determine the risk of re-introduction of PEDV if it were regionally eliminated. Ongoing molecular surveillance is essential to confirming that some older clades no longer circulate anymore in the U.S., mapping the distribution and spread of recent clades, and understanding PEDV’s evolutionary diversification.

Senecavirus A (SVA) is an endemic pathogen with ongoing relevance to the U.S. swine industry due to its clinical resemblance to foot-and-mouth disease (FMD) and its potential impact on animal health and trade. This study analyzes the incidence and geographic distribution of SVA outbreaks in U.S. breeding herds from January 2015 to December 2024. We used enhanced surveillance by combining diagnostic data from veterinary diagnostic laboratories and practitioners’ reports to assess SVA incidence, identifying temporal fluctuations and regional patterns. Our findings indicate that the cumulative incidence of SVA in U.S. breeding herds is low overall (<2.5% per year), with peak incidence observed during the third and fourth quarters of the calendar year. Outbreaks are more frequently reported in the Midwest. Our results suggest potential seasonality or regional factors influencing disease transmission. The median time interval between SVA outbreaks for sites experiencing more than one outbreak is 402 days. This study provides valuable insights into the current epidemiology of SVA in U.S. breeding herds, and highlights the need for continued monitoring and preparedness to prevent future outbreaks.

Assessing whether post mortem samples can provide value for monitoring during the post-weaning stages is necessary as this methodology can be adopted by the industry when resources are scarce. The objectives of this study are to assess pathogen detection in tongue tip fluids (TTFs), oronasal swabs (ONSs), rectal swabs (RSs), and superficial inguinal lymph nodes (SILNs). Two farms (one wean-to-finish farm and one finishing farm) undergoing a porcine reproductive and respiratory syndrome virus (PRRSV) outbreak were included, and 30 dead pigs were sampled during each farm visit. For PRRSV, the diagnostic accuracy of TTF, ONS, RS, and SILN were calculated using intracardiac serum as the gold standard. We also characterized the detection of PCV-2, PCV-3, PPV-1, PPV-2, Lawsonia intracellularis, and IAV in all collected specimens. Overall, TTF and SILN had the highest sensitivity for PRRSV-2 detection (95% and 99%, respectively). Most other pathogens were detected in TTF, with the highest detection rates were for PPV-2 (99%) and PCV-2 (41%). RS had mostly good detection rates for PPV-2 (27–73%), while ONS had similar detection rates (37%) to TTF (38%) for IAV. Altogether, this indicates that post mortem specimens can provide value for pathogen detection.