Factors associated with cow- and herd-level somatic cell count patterns on organic dairy farms in the United States

The objective of this study was to characterize cow- and herd-level patterns of somatic cell counts (SCC) in organic-certified cows enrolled in the DHI program, considering cow (parity, DIM, milk yield, and breed), herd (herd size), and environmental factors (geographic region, year, and season). The data set comprised 2,327,479 test-day records collected between 2018 and 2025 from 430 organic-certified dairy farms enrolled in the DHI program through the Dairy Records Management Systems, representing a total of 364,413 lactations. To evaluate potential associations at the cow-level between SCC and the variables of interest, separate linear mixed models were fitted for interactions between pairs of explanatory variables using natural log-transformed SCC (LnSCC). Additionally, relative frequencies of observations across SCC categories (≤100,000, 101,000-200,000, 201,000-500,000, 501,000-1,000,000, and >1,000,000 cells/mL) were calculated for each level of the categorical variables evaluated. For the herd-level analysis, mean herd SCC was calculated for each herd-year-season combination, and relative frequencies across SCC categories were estimated. Cumulative link mixed models for ordinal outcomes were used to assess herd-level associations between variables of interest and SCC categories, by calculating the probabilities of herds falling into higher ordinal SCC categories across explanatory variable levels. The cow-level results were back-transformed to the original SCC scale for presentation purposes, indicating that SCC increased with parity and varied throughout the lactation, peaking in early lactation (0-30 DIM), decreasing during mid-lactation (31-100 DIM), and gradually increasing again toward late lactation. Cows in the lowest quartile of relative milk yield consistently exhibited higher SCC across DIM categories compared with cows in the higher quartiles of MY. Holsteins had the lowest SCC, whereas Jersey and other breeds had higher values. Seasonal effects were evident, with SCC peaking during summer, particularly from July to September, and cows in the Midwest showing lower SCC than those in the Northeast, South, and West. SCC were highest in large herds (>500 cows) and lowest in medium-sized herds (101-500 cows). Similarly, the proportion of cows in the lowest SCC category (<100,000 cells/mL) decreased with increasing parity and was lower during early and late lactation and during the summer months. Holsteins had the highest proportion of cows in the lowest SCC category. Larger herds and farms located in the South and West showed greater proportions of cows in SCC categories above 200,000 cells/mL. Over the last 3 years of the study period, the proportion of observations in SCC >200,000 cells/mL increased in large herds and on farms in the South and West but declined in medium-sized herds (101-500 cows). At the herd-level analysis, larger herds and farms located in the South had a greater probability of being classified into higher SCC categories than smaller herds and farms located in the other 3 regions, respectively. Additionally, the probability of higher SCC categories was greater during the hot season than during the cold season. Overall, multiple variables were associated with the cow- and herd-level patterns of SCC in US organic-certified dairies, reflecting the combined effects of cow physiology, herd characteristics, seasonal patterns, and regional environmental conditions.