Cross-sectional study of the relationships among bedding materials, bedding bacteria counts, and intramammary infection in late-lactation dairy cows

Comparison of a machine learning model with a conventional rule-based selective dry cow therapy algorithm for detection of intramammary infections

We trained machine learning models to identify intramammary infections (IMI) in late lactation cows at dry-off to guide antibiotic treatment, and compared their performance to a rule-based algorithm that is currently used on dairy farms in the US. We conducted an observational test-characteristics study using a data set of 3,645 cows approaching dry-off from 68 US dairy herds. The outcome variables of interest were cow-level IMI caused by all pathogens, major pathogens, and Streptococcus and Strep-like organisms (SSLO), which were determined using aerobic culture of aseptic quarter-milk samples and identification of isolates using MALDI-TOF. Individual cow records were extracted from the farm software to create 53 feature variables at the cow and 39 at the herd-level which were derived from cow-level descriptive data, records of clinical mastitis events, results from routine testing of milk for volume and concentrations of somatic cell count (SCC), fat, and protein. ML algorithms evaluated were logistic regression, decision tree, random forest, light gradient-boosting machine, naïve bayes, and neural networks. For comparison, cows were also classified according to a conventional rule-based algorithm that considered a cow as high risk for IMI if she had at one or more high SCC (>200,000 cells/ml) tests or ≥2 cases of clinical mastitis during the lactation of enrollment. Area under the curve (AUC) and Youden's index were used to compare models, in addition to binary classification metrics, including sensitivity, specificity, and predictive values. ML models had slightly higher AUC and Youden's index values than the rule-based algorithm for all IMI outcomes of interest. However, these improvements in prediction accuracy were substantially less than what we had considered necessary for the technology to be a worthwhile alternative to the rule-based algorithm. Therefore, evidence is lacking to support the wholesale use of ML-guided selective dry cow therapy at the moment. We recommend that producers wanting to implement algorithm-guided SDCT use a rule-based method.

Validity of luminometry and bacteriological tests for diagnosing intramammary infection at dry-off in dairy cows

The objective of this cross-sectional study was to estimate the validity of laboratory culture, Petrifilm and Tri-Plate on-farm culture systems, as well as luminometry to correctly identify IMI at dry-off in dairy cows, considering all tests to be imperfect. From September 2020 until December 2021, we collected composite milk samples from cows before dry-off and divided them into 4 aliquots for luminometry, Petrifilm (aerobic count), Tri-Plate, and laboratory culture tests. We assessed multiple thresholds of relative light units (RLU) for luminometry, and we used thresholds of ≥100 cfu/mL for the laboratory culture, ≥50 cfu/mL for Petrifilm, and ≥1 cfu for Tri-Plate tests. We fitted Bayesian latent class analysis models to estimate the sensitivity (Se) and specificity (Sp) for each test to identify IMI, with 95% credibility interval (BCI). Using different prevalence measures (0.30, 0.50, and 0.70), we calculated the predictive values (PV) and misclassification cost terms (MCT) at different false negative-to-false-positive ratios (FN:FP). A total of 333 cows were enrolled in the study from one commercial Holstein herd. The validity of the luminometry was poor for all thresholds, with an Se of 0.51 (95% BCI = 0.43-0.59) and Sp of 0.38 (95% BCI = 0.26-0.50) when using a threshold of ≥150 RLU. The laboratory culture had an Se of 0.93 (95% BCI = 0.85-0.98) and Sp of 0.69 (95% BCI = 0.49-0.89); the Petrifilm had an Se of 0.91 (95% BCI = 0.80-0.98) and Sp of 0.71 (95% BCI = 0.51-0.90); and the Tri-Plate had an Se of 0.65 (95% BCI = 0.53-0.82) and Sp of 0.85 (95% BCI = 0.66-0.97). Bacteriological tests had good PV, with comparable positive PV for all 3 tests, but lower negative PV for the Tri-Plate compared with the laboratory culture and the Petrifilm. For a prevalence of IMI of 0.30, all 3 tests had similar MCT, but for prevalence of 0.50 and 0.70, the Tri-Plate had higher MCT in scenarios where leaving a cow with IMI untreated is considered to have greater detrimental effects than treating a healthy cow (i.e., FN:FP of 3:1). Our results showed that the bacteriological tests have adequate validity to diagnose IMI at dry-off, but luminometry does not. We concluded that although luminometry is not useful to identify IMI at dry-off, the Petrifilm and Tri-Plate tests performed similarly to laboratory culture, depending on the prevalence and importance of the FP and FN results.

Effect of double-premilking teat disinfection protocols on bacterial counts on teat skin of cows and milker gloves in a free-stall-housed dairy herd

This research communication addresses the hypothesis that double premilking teat disinfection (DD) is more effective in reducing soiling and bacterial count on the cows' teat skin and milkers' gloves than conventional disinfection (CONV). The design was a 3 × 3 Latin square (three groups of cows and three treatments) with conventional teat disinfection (CONV, lactic acid application after forestripping), double teat disinfection using the same disinfectant (DD1D, lactic acid application before and after forestripping), and double teat disinfection using two different disinfectants (DD2D, application of lactic acid before and chlorine-based disinfectant after forestripping). All groups were assigned for six days for each treatment, and the evaluations and samples were collected on the last day, before and after treatment. We evaluated the teat cleanliness score (TCS), count of Gram-negative bacteria (coliforms and noncoliforms), Staphylococcus spp., Streptococcus spp., and total bacterial count (TBC) on the cows' teats and TBC on the milkers' gloves. TCS after premilking was lower in DD than CONV treatment. The reduction of Staphylococcus spp. count was greater in the DD treatment and tended to be higher in the DD2D. The TBC reduction on the cows' teats was greater in the DD treatments. The TBC on the milkers' gloves was lower for DD before and after premilking. In conclusion, DD can be an alternative for reducing some bacterial populations on cow teats and preventing the transmission of microorganisms between cows via the milkers' hands.

Intramammary infections in lactating Jersey cows: Prevalence of microbial organisms and association with milk somatic cell count and persistence of infection

There are limited data available regarding pathogens causing intramammary infections (IMI) in Jersey cows. The objectives of this study were to characterize the prevalence of IMI caused by different microorganisms in lactating Jersey cattle and evaluate the associations among microbes and somatic cell count (SCC) and persistence of IMI. This prospective, observational, longitudinal study included lactating Jersey cows (n = 753) from 4 farms within a 415 km radius of Columbia, Missouri. Quarter foremilk samples were aseptically collected monthly for 3 consecutive months. Microorganisms were identified using aerobic milk culture and MALDI-TOF mass spectrometry. A commercial laboratory measured SCC using flow cytometry. Milk culture results were used to classify single microorganism infections as persistent (same microorganism species identified at first sampling and one other sampling) or nonpersistent infection. Mixed models were built to evaluate the associations between IMI status and SCC natural logarithm (lnSCC), as well as persistence and lnSCC. Overall, staphylococci were the most commonly isolated microorganisms among the 7,370 quarter-level milk samples collected. Median prevalence (using all 3 samplings) of specific microbes varied among farms; however, Staphylococcus chromogenes was a common species found at all farms. The most common microbial species that persisted were Staph. chromogenes, Staphylococcus aureus, Staphylococcus simulans, and Streptococcus uberis. Streptococcus dysgalactiae and Staph. aureus were the IMI associated with the most inflammation based on lnSCC. The small number of herds included in this study with the large variation in herd type limits the generalizability of the data. However, results of this study seem to be similar to those of previous studies in other breeds, suggesting management factors are more important than breed-specific differences when evaluating causes of IMI and associated subclinical mastitis.

Pathogen group-specific risk factors for intramammary infection in water buffalo

A cross-sectional study was conducted to estimate the prevalence of intramammary infection (IMI) associated bacteria and to identify risk factors for pathogen group-specific IMI in water buffalo in Bangladesh. A California Mastitis Test (CMT) and bacteriological cultures were performed on 1,374 quarter milk samples collected from 763 water buffalo from 244 buffalo farms in nine districts in Bangladesh. Quarter, buffalo, and farm-related data were obtained through questionnaires and visual observations. A total of 618 quarter samples were found to be culture positive. Non-aureus staphylococci were the predominant IMI-associated bacterial species, and Staphylococcus (S.) chromogenes, S. hyicus, and S. epidermidis were the most common bacteria found. The proportion of non-aureus staphylococci or Mammaliicoccus sciuri (NASM), S. aureus, and other bacterial species identified in the buffalo quarter samples varied between buffalo farms. Therefore, different management practices, buffalo breeding factors, and nutrition were considered and further analyzed when estimating the IMI odds ratio (OR). The odds of IMI by any pathogen (OR: 1.8) or by NASM (OR: 2.2) was high in buffalo herds with poor milking hygiene. Poor cleanliness of the hind quarters had a high odds of IMI caused by any pathogen (OR: 2.0) or NASM (OR: 1.9). Twice daily milking (OR: 3.1) and farms with buffalo purchased from another herd (OR: 2.0) were associated with IMI by any pathogen. Asymmetrical udders were associated with IMI-caused by any bacteria (OR: 1.7). A poor body condition score showed higher odds of IMI by any pathogen (OR: 1.4) or by NASM (OR: 1.7). This study shows that the prevalence of IMI in water buffalo was high and varied between farms. In accordance with the literature, our data highlight that IMI can be partly controlled through better farm management, primarily by improving hygiene, milking management, breeding, and nutrition.

Negatively controlled trial investigating the effects of dry cow therapy on clinical mastitis and culling in multiparous cows

Blanket dry cow therapy (DCT) is a major contributor to overall antibiotic usage on dairy farms in the United States. With low prevalence of intramammary infections at dry-off in US herds today, alternative DCT approaches have been the focus of much research. We hypothesized that complete cessation of DCT [i.e., use of internal teat sealants (ITS) only at dry-off] could be a practical alternative to blanket DCT in well-managed herds. The objective of this negatively controlled clinical trial was to determine the effects of DCT on clinical mastitis (CM) and removal from the herd during the dry period and the first 200 d of the subsequent lactation in multiparous dairy cows treated with only ITS at dry-off. As a secondary objective, we conducted exploratory analysis to identify subpopulations in the herd (based on parity, previous CM history, and dry-period length) where DCT would not affect postcalving udder health, to generate hypotheses about potential alternative selective DCT programs. The study was conducted in a commercial dairy herd in South Dakota from June 2020 to January 2021. Dry-off sessions (n = 43) were scheduled such that all cows at a given session were dried off using ITS alone (ITS only, n = 20 sessions, n = 1,108 cows) or an intramammary DCT product containing 500 mg of cloxacillin (Dry-Clox, Boehringer Ingelheim) followed by ITS (ITS+ABX, n = 23 sessions, n = 1,331 cows). Culling and CM events were recorded by farm workers who were blinded to the treatment status of cows. Hazard ratios (HR) for the effects of the treatment group on CM and removal from the herd were estimated using multivariable Cox proportional hazards, adjusting for the clustered treatment allocation strategy. Risk of removal from the herd during the dry period was lower in ITS+ABX than ITS-only cows (1.1 vs. 2.7%; HR = 0.45; 95% CI: 0.25 to 0.81). Risk of removal from the herd during the first 200 d of lactation was similar in ITS+ABX and ITS-only cows (17.3 vs. 18.0%; HR = 0.98; 95% CI: 0.82 to 1.18). Risk of CM during the first 200 d of lactation was lower in ITS+ABX cows (6.9%; HR = 0.56; 95% CI: 0.41 to 0.76) compared with ITS-only cows (13.4%). The beneficial effects of DCT on CM and removal from the herd were consistently observed across strata of parity, previous CM history, and dry-period length, indicating that no subpopulations could be identified to withhold DCT. The findings from this study indicate that the omission of DCT from the dry-off procedure, when udder health is not taken into consideration, in multiparous cows can have a negative effect on cow health and welfare. Findings from previous research suggest that culture- or algorithm-guided selective dry cow therapy are likely to be safer approaches to improving antibiotic stewardship.

Diagnosing Intramammary Infection: Meta-Analysis and Mapping Review on Frequency and Udder Health Relevance of Microorganism Species Isolated from Bovine Milk Samples

Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry provides accurate species-level identification of many, microorganisms retrieved from bovine milk samples. However, not all those microorganisms are pathogenic. Our study aimed to: (1) determine the species-specific prevalence of microorganisms identified in bovine milk of apparently healthy lactating quarters vs. quarters with clinical mastitis (CM); and (2) map current information and knowledge gaps on udder health relevance of microorganisms retrieved from bovine milk samples. A mixed study design (meta-analysis and mapping review) was chosen. We gathered several large Canadian, US and Brazilian data sets of MALDI-TOF results for organisms cultured from quarter milk samples. For meta-analysis, two datasets (apparently healthy quarters vs. CM samples) were organized. A series of meta-analyses was conducted to determine microorganisms' prevalence. Then, each species reported was searched through PubMed to investigate whether inflammation (increased somatic cell count (SCC) or signs of CM) was associated with microorganism's recovery from milk. A total of 294 different species of microorganisms recovered from milk samples were identified. Among 50,429 quarter-milk samples from apparently healthy quarters, the 5 most frequent species were Staphylococcus chromogenes (6.7%, 95% CI 4.5-9.2%), Aerococcus viridans (1.6%, 95% CI 0.4-3.5%), Staphylococcus aureus (1.5%, 95% CI 0.5-2.8%), Staphylococcus haemolyticus (0.9%, 95% CI 0.4-1.5%), and Staphylococcus epidermidis (0.7%, 95% CI 0.2-1.6%). Among the 43,924 quarter-milk CM samples, the 5 most frequent species were Escherichia coli (11%, 95% CI 8.1-14.3%), Streptococcus uberis (8.5%, 95% CI 5.3-12.2%), Streptococcus dysgalactiae (7.8%, 95% CI 4.9-11.5%), Staphylococcus aureus (7.8%, 95% CI 4.4-11.9%), and Klebsiella pneumoniae (5.6%, 95% CI 3.4-8.2%). When conducting the PubMed literature search, there were 206 species identified by MALDI-TOF for which we were not able to find any information regarding their association with CM or SCC. Some of them, however, were frequently isolated in our multi-country dataset from the milk of quarters with CM (e.g., Citrobacter koseri, Enterococcus saccharolyticus, Streptococcus gallolyticus). Our study provides guidance to veterinarians for interpretation of milk bacteriology results obtained using MALDI-TOF and identifies knowledge gaps for future research.

Invited review: Selective use of antimicrobials in dairy cattle at drying-off

Administering intramammary antimicrobials to all mammary quarters of dairy cows at drying-off [i.e., blanket dry cow therapy (BDCT)] has been a mainstay of mastitis prevention and control. However, as udder health has considerably improved over recent decades with reductions in intramammary infection prevalence at drying-off and the introduction of teat sealants, BDCT may no longer be necessary on all dairy farms, thereby supporting antimicrobial stewardship efforts. This narrative review summarizes available literature regarding current dry cow therapy practices and associated impacts of selective dry cow therapy (SDCT) on udder health, milk production, economics, antimicrobial use, and antimicrobial resistance. Various methods to identify infections at drying-off that could benefit from antimicrobial treatment are described for selecting cows or mammary quarters for treatment, including utilizing somatic cell count thresholds, pathogen identification, previous clinical mastitis history, or a combination of criteria. Selection methods may be enacted at the herd, cow, or quarter levels. Producers' and veterinarians' motivations for antimicrobial use are discussed. Based on review findings, SDCT can be adopted without negative consequences for udder health and milk production, and concurrent teat sealant use is recommended, especially in udder quarters receiving no intramammary antimicrobials. Furthermore, herd selection should be considered for SDCT implementation in addition to cow or quarter selection, as BDCT may still be temporarily necessary in some herds for optimal mastitis control. Costs and benefits of SDCT vary among herds, whereas impacts on antimicrobial resistance remain unclear. In summary, SDCT is a viable management option for maintaining udder health and milk production while improving antimicrobial stewardship in the dairy industry.

Evaluation of Contamination in Milk Samples Pooled From Independently Collected Quarters Within a Laboratory Setting

The primary objective of this observational study was to evaluate the prevalence of contamination from independently collected quarter-level milk samples pooled in a laboratory and subjected to bacterial culture. To address this objective, weekly quarter-level milk samples were collected longitudinally from a cohort of 503 primiparous cows from five organic dairy farms during the first 5 weeks after calving. Individual quarter milk samples were pooled in a laboratory using aseptic technique (“lab-pooled”) and subjected to bacterial culture. In the sample set of 2,006 lab-pooled milk samples, 207 (10.3%) were classified as contaminated using a standard definition (i.e., growth of three or more distinct microorganisms). Subsequent culturing of corresponding quarter-level milk samples revealed that many of the contaminated lab-pooled sample results (i.e., 46.7%) were the result of intramammary infections with different pathogens across the quarters, rather than actual contamination within any single quarter (i.e., “true contamination”). The odds of true contamination were lower when the lab-pooled sample exhibited growth of three microorganisms compared to more than 3 microorganisms. Our findings suggest that pooling of quarter samples within a laboratory setting may yield lower rates of contamination compared to those previously reported from samples composited on-farm, but that current cut-offs to define contamination may need to be evaluated for use with lab-pooled samples. Further investigation of use of lab-pooled samples may be warranted to reduce costs while still providing useful scientific insight.

Distribution of staphylococcal and mammaliicoccal species from compost-bedded pack or sand-bedded freestall dairy farms

The purpose of this prospective observational study was to determine whether dairy cattle housing types were associated with staphylococcal and mammaliicoccal populations found on teat skin, bedding, and in bulk tank milk. Twenty herds (n = 10 sand-bedded freestall herds; n = 10 compost-bedded pack herds) were enrolled. Each herd was visited twice for sample collection, and at each visit, 5 niches were sampled, including bulk tank milk, composite teat skin swab samples collected before premilking teat preparation, composite teat skin swab samples collected after premilking teat preparation, unused fresh bedding, and used bedding. All samples were plated on Mannitol salt agar and Columbia blood agar and staphylococcal-like colonies were selected for further evaluation. Bacterial colonies were speciated using MALDI-TOF mass spectrometry. All species were grouped into 4 categories included host-adapted, opportunistic, environmental, and unclassified. Absolute numbers and proportions of each genus and species were calculated. Proportional data were compared between groups using Fisher's exact test. Data representing 471 staphylococcal-like organisms were analyzed. Overall, 27 different staphylococcal and mammaliicoccal species were identified. Staphylococcus chromogenes was the only species identified from all 20 farms. A total of 20 different staphylococcal-like species were identified from bulk tank milk samples with the most prevalent species being S. chromogenes, followed by Staphylococcus aureus and Mammaliicoccus sciuri. Overall, more staphylococcal and mammaliicoccal isolates were identified among used bedding than unused bedding. The increased numbers of isolates within used bedding were primarily from used sand bedding samples, with 79% (76/96) of used bedding isolates being identified from sand bedding and only 20.8% (20/96) from used compost-bedded pack samples. When comparing categories found among sample types, more unclassified species were found in used sand bedding than in used compost-bedded pack samples. This finding is possibly related to the composting temperatures resulting in reduced growth or destruction of bacterial species. The prevalence of S. aureus was high in bulk tank milk for all herds, regardless of herd type, which may represent the influence of unmeasured management factors. Overall, staphylococcal and mammaliicoccal species were highly prevalent among samples from both farm types.

The microbiome of common bedding materials before and after use on commercial dairy farms

Background

Bovine mastitis is one of the most economically important diseases affecting dairy cows. The choice of bedding material has been identified as an important risk factor contributing to the development of mastitis. However, few reports examine both the culturable and nonculturable microbial composition of commonly used bedding materials, i.e., the microbiome. Given the prevalence of nonculturable microbes in most environments, this information could be an important step to understanding whether and how the bedding microbiome acts as a risk factor for mastitis. Therefore, our objective was to characterize the microbiome composition and diversity of bedding material microbiomes, before and after use.

Methods

We collected 88 bedding samples from 44 dairy farms in the U.S. Unused (from storage pile) and used (out of stalls) bedding materials were collected from four bedding types: new sand (NSA), recycled manure solids (RMS), organic non-manure (ON) and recycled sand (RSA). Samples were analyzed using 16S rRNA sequencing of the V3–V4 region.

Results

The overall composition as well as the counts of several microbial taxa differed between bedding types, with Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes dominating across all types. Used bedding contained a significantly different microbial composition than unused bedding, but the magnitude of this difference varied by bedding type, with RMS bedding exhibiting the smallest difference. In addition, positive correlations were observed between 16S rRNA sequence counts of potential mastitis pathogens (bacterial genera) and corresponding bedding bacterial culture data.

Conclusion

Our results strengthen the role of bedding as a potential source of mastitis pathogens. The consistent shift in the microbiome of all bedding types that occurred during use by dairy cows deserves further investigation to understand whether this shift promotes pathogen colonization and/or persistence, or whether it can differentially impact udder health outcomes. Future studies of bedding and udder health may be strengthened by including a microbiome component to the study design.

Supplementary Information

The online version contains supplementary material available at 10.1186/s42523-022-00171-2.

Effect of Peanut Shell and Rice Husk Bedding for Dairy Cows: An Analysis of Material Properties and Colostrum Microbiota

Simple Summary

The provision of appropriate bedding is important for the welfare of dairy cows. Before bedding can be selected, it is critical to understand the properties of the bedding, including its impact on milk microbiota. The objective of this article was to evaluate the influence of three materials for use as bedding on physicochemical properties, bacterial counts and colostrum microbiota of cows. Our results demonstrate that peanut shells appear to be a suitable bedding material for cows. These experiments provide empirical support for the use of peanut shells and rice husks as bedding material for dairy cows and illustrates the effects of bedding types on the colostrum microbiota of dairy cows.

Abstract

The aim of this study was to evaluate peanut shells and rice husks as bedding for dairy cows. We analyzed material properties including dry matter, water holding capacity, pH level and bacterial counts. Bedding treatments were compared with a one-way ANOVA using twelve cows split into three groups. Colostrum microbiota was analyzed by sequencing of the V3–V4 region of the 16S rRNA gene. Dry matter content was higher in rice husks compared with peanut shells. No treatment effects were found for water holding capacity and pH level. Streptococcus agalactia counts in peanut shell bedding were lower than in rice husk bedding, and Pseudomonas aeruginosa counts were not different between beddings. A significant enrichment for Enhydrobacter and Pantoea were detected in the colostrum of cows that used peanut shells compared with other beddings. Colostrum of cows housed on a peanut–rice combination had a greater relative abundance of Pseudomonas and Corynebacterium than those housed on peanut shells or rice husks. Higher numbers of Bacteroides, Akkermansia, Alistipes, Ruminococcaceae_UCG-014, Coriobacteriaceae_UCG-002 and Intestinimona were found in the colostrum of cows housed on rice husk bedding over other bedding types. These results suggest that bedding types were associated with the growth and diversity of colostrum bacterial loads. In addition, dry matter in peanut shells was lower than found in rice husks, but there was also a lower risk of mastitis for peanut shell bedding than other beddings.

A survey of mastitis pathogens including antimicrobial susceptibility in southeastern Australian dairy herds

The objectives for this study were to (1) describe the pathogen profile in quarters from cows with clinical mastitis and in cows with subclinical mastitis in southeastern Australia; and (2) describe antimicrobial susceptibility among isolated pathogens. As a secondary objective, we aimed to compare antimicrobial resistance prevalence in pathogens isolated from clinical and subclinical mastitis samples. A convenience sample of dairy herds (n = 65) from 4 regions in southeastern Australia (Gippsland, Northern Victoria, Tasmania, Western Victoria) were invited to submit milk samples from cows with clinical and subclinical mastitis over a 14-mo period (January 2011 to March 2012). Farmers were instructed to collect aseptic quarter milk samples from the first 10 cases of clinical mastitis for each month of the study. In addition, farmers submitted composite milk samples from cows with subclinical mastitis at 1 or 2 sampling occasions during the study period. Aerobic culture and biochemical tests were used to identify isolates. Isolates were classified as susceptible, intermediate, or resistant to a panel of antimicrobial agents based on the zone of growth inhibition around antimicrobial-impregnated disks, with antimicrobial resistance (AMR) classified as nonsusceptibility by combining intermediate and resistant groups into a single category. Generalized linear mixed models were used to compare the prevalence of AMR between clinical and subclinical mastitis isolates. For clinical mastitis samples (n = 3,044), 472 samples (15.5%) were excluded for contamination. Of the remaining samples (n = 2,572), the most common results were Streptococcus uberis (39.2%), no growth (27.5%), Staphylococcus aureus (10.6%), Escherichia coli (8.4%), and Streptococcus dysgalactiae (6.4%). For subclinical mastitis samples (n = 1,072), 425 (39.6%) were excluded due to contamination. Of the remaining samples (n = 647), the most common results were no growth (29.1%), Staph. aureus (29.1%), and Strep. uberis (21.6%). The prevalence of AMR among common isolates was low for the majority of antimicrobial agents. Exploratory analysis found that the probability of Staph. aureus demonstrating resistance to penicillin was 5.16 times higher (95% confidence interval: 1.68, 15.88) in subclinical isolates relative to clinical Staph. aureus isolates. A similar association was observed for amoxicillin with subclinical Staph. aureus isolates being 4.70 times (95% confidence interval: 1.49, 14.75) more likely to be resistant than clinical Staph. aureus isolates. We concluded that the most common bacteria causing clinical mastitis in dairy herds in Australia is likely to be Strep. uberis, whereas Staph. aureus is likely to be the most common cause of subclinical mastitis. Despite decades of antimicrobial use to control these organisms, AMR appears to be uncommon.

Comparison of microbiota of recycled manure solids and straw bedding used in dairy farms in eastern Canada

Recycled manure solids (RMS) bedding is an alternative bedding option that is growing in popularity on Canadian dairy farms. However, the microbiological characteristics and production of RMS bedding are poorly documented under on-farm conditions in eastern Canada. This bedding could support the presence of pathogens and could have an effect on cow and human health. The aim of this study was to describe the RMS microbiota when used under dairy cows and compare it with straw bedding. Unused and used bedding from 27 RMS and 61 straw-bedded dairy farms were collected and compared using 16S amplicon sequencing, bacterial counts, and Salmonella spp. and Listeria monocytogenes detection. Microbiota composition of unused RMS and unused straw were different. After use, both bedding microbiota were similar in their bacterial composition, structure, and diversity. Unused RMS generally contained higher bacterial counts than did unused straw, except for Klebsiella spp. counts. Salmonella spp. and L. monocytogenes were more frequently detected in unused RMS (Salmonella spp.: 11%; L. monocytogenes: 30%), than in unused straw (Salmonella spp.: 0%; L. monocytogenes: 11%). Finally, 2 RMS production systems (extraction of the liquid fraction followed by maturation in an opened or enclosed container vs. in a heap) did not influence the microbiota richness and bacteria distribution (α-diversity), but did influence the microbiota structure (β-diversity). In conclusion, animal and human pathogens were found in greater numbers and more frequently in unused RMS than unused straw, and this could eventually affect dairy cow or human health.

Evaluation of 4 predictive algorithms for intramammary infection status in late-lactation cows

The objective of this observational study was to compare 4 cow-level algorithms to predict cow-level intramammary infection (IMI) status (culture and MALDI-TOF) in late-lactation US dairy cows using standard measures of test performance. Secondary objectives were to estimate the likely effect of each algorithm, if used to guide selective dry cow therapy (SDCT), on dry cow antibiotic use in US dairy herds, and to investigate the importance of including clinical mastitis criteria in algorithm-guided SDCT. Cows (n = 1,594) from 56 US dairy herds were recruited as part of a previously published cross-sectional study of bedding management and IMI in late-lactation cows. Each herd was visited twice for sampling. At each farm visit, aseptic quarter-milk samples were collected from 20 cows approaching dry-off (>180 d pregnant), which were cultured using standard bacteriological methods and MALDI-TOF for identification of isolates. Quarter-level culture results were used to establish cow-level IMI status, which was considered the reference test in this study. Clinical mastitis records and Dairy Herd Improvement Association test-day somatic cell count data were extracted from herd records and used to perform cow-level risk assessments (low vs. high risk) using 4 algorithms that have been proposed for SDCT in New Zealand, the Netherlands, United Kingdom, and the United States. Agreement between aerobic culture (reference test; IMI vs. no-IMI) and algorithm status (high vs. low risk) was described using Cohen's kappa, test sensitivity, specificity, negative predictive value, and positive predictive value. The proportion of cows classified as high risk among the 4 algorithms ranged from 0.31 to 0.63, indicating that these approaches to SDCT could reduce antibiotic use at dry-off by 37 to 69% in the average US herd. All algorithms had poor agreement with IMI status, with kappa values ranging from 0.05 to 0.13. Sensitivity varied by pathogen, with higher values observed when detecting IMI caused by Streptococcus uberis, Streptococcus dysgalactiae, Staphylococcus aureus, and Lactococcus lactis. Negative predictive values were high for major pathogens among all algorithms (≥0.87), which may explain why algorithm-guided SDCT programs have been successfully implemented in field trials, despite poor agreement with overall IMI status. Removal of clinical mastitis criteria for each algorithm had little effect on the algorithm classification of cows, indicating that algorithms based on SCC alone may have similar performance to those based on SCC and clinical mastitis criteria. We recommend that producers implementing algorithm-guided SDCT use algorithm criteria that matches their relative aspirations for reducing antibiotic use (high specificity, positive predictive value) or minimizing untreated IMI at dry-off (high sensitivity, negative predictive value).

Description of the Characteristics of Five Bedding Materials and Association With Bulk Tank Milk Quality on Five New York Dairy Herds

Environmental mastitis represents a major challenge on dairy farms where contagious pathogens are controlled by improved milking procedures. Therefore, research focused on the environment is important to improve udder health programs. The objectives of this prospective and descriptive study were to (1) describe bedding bacterial counts, pH, and dry matter (DM) of five different bedding types (organic: manure solids, straw, paper fiber; inorganic: sand, recycled sand) and (2) explore the association between bedding bacterial counts with bulk tank milk quality. This study took place within five conveniently selected commercial dairy herds, each with a predominant bedding material in lactating pens. Bedding samples (used n = 237; fresh n = 53) were collected monthly from July 2018 to July 2019 following a standard operating procedure (SOP) to minimize sampling variability. Additionally, a bulk tank (BT) milk sample (n = 40) was collected on the same day unless milk had been picked up prior to arrival. Both BT and bedding samples were submitted to the laboratory for culture and bacterial identification and quantification of Streptococcus spp, coliforms, and non-coliforms as well as detection of several pathogens of mastitis importance. Somatic cell count was evaluated in BT samples. Within bedding type, the correlation between bedding characteristics and bacterial counts in bedding was evaluated using Pearson correlation. Within bedding type, the correlation between bacterial counts in bedding samples and bacterial counts in BT were determined. The Kruskal–Wallis test was used to evaluate the bacterial count by bedding type and to evaluate BT somatic cell count differences based on bedding type. In fresh bedding, bacterial counts were generally higher for manure solids for all bacterial groups compared with other materials. In used samples, organic materials had the highest levels of all bacterial groups. The proportion of samples with detectable organisms of mastitis importance varied within and among herds in both bedding and BT samples throughout the study period. In bedding samples, a higher DM content had the lowest levels of bacterial growth compared with those with lower DM content. Most bedding samples were on the alkaline side within a pH range of 8–11. No relationship between bacterial counts and pH was observed. No associations between BT bacteria counts and bedding bacterial counts were observed. No association between bulk tank somatic cell counts based on bedding type were observed. Despite using an SOP for bedding sampling in an effort to consistently collect samples, we still observed a large amount of variability both within and among bedding samples. This variability may have obscured any potential association between BT milk quality and bedding type.

Partial budget analysis of culture- and algorithm-guided selective dry cow therapy

The objectives of this study were to (1) use partial budget analysis to estimate the cash impact for herds that switch from blanket dry cow therapy (BDCT) to culture- or algorithm-guided selective dry cow therapy (SDCT) and (2) conduct a sensitivity analysis to investigate effects in situations where SDCT increased clinical and subclinical mastitis risk during the subsequent lactation. A partial budget model was created using Monte Carlo simulation with @Risk software. Expenditures associated with dry-off procedures and health outcomes (clinical and subclinical mastitis) during the first 30 d in milk were used to model herd-level effects, expressed in units of US dollars per cow dry-off. Values for each economic component were derived from findings from a recent multisite clinical trial, peer-reviewed journal articles, USDA databases, and our experiences in facilitating the implementation of SDCT on farms. Fixed values were used for variables expected to have minimal variation within the US dairy herd population (e.g., cost of rapid culture plates) and sampling distributions were used for variables that were hypothesized to vary enough to effect the herd net cash impact of one or more DCT approach(es). For Objective 1, herd-level udder health was assumed to be unaffected by the implementation of SDCT. For culture-guided SDCT, producers could expect to save an average of +$2.14 (-$2.31 to $7.23 for 5th and 95th percentiles) per cow dry-off as compared with BDCT, with 75.5% of iterations being ≥$0.00. For algorithm-guided SDCT, the mean net cash impact was +$7.85 ($3.39-12.90) per cow dry-off, with 100% of iterations being ≥$0.00. The major contributors to variance in cash impact for both SDCT approaches were percent of quarters treated at dry-off and the cost of dry cow antibiotics. For Objective 2, we repeated the partial budget model with the 30-d clinical and subclinical mastitis incidence increasing by 1, 2, and 5% (i.e., risk difference = 0.01, 0.02, and 0.05) in both SDCT groups compared with BDCT. For algorithm-guided SDCT, average net cash impacts were ≥$0.00 per cow dry-off (i.e., cost effective) when mastitis incidence increased slightly. However, as clinical mastitis incidence increased, economic returns for SDCT diminished. These findings indicate that when SDCT is implemented appropriately (i.e., no to little negative effect on health), it might be a cost-effective practice for US herds under a range of economic conditions.

Postcalving udder health and productivity in cows approaching dry-off with intramammary infections caused by non-aureus Staphylococcus, Aerococcus, Enterococcus, Lactococcus, and Streptococcus species

The objective of this prospective cohort study was to explore associations between intramammary infection (IMI) in late-lactation cows and postcalving udder health and productivity. Cows (n = 2,763) from 74 US dairy herds were recruited as part of a previously published cross-sectional study of bedding management and IMI in late-lactation cows. Each herd was visited twice for sampling. At each visit, aseptic quarter milk samples were collected from 20 cows approaching dry-off (>180 d pregnant), which were cultured using standard bacteriological methods and MALDI-TOF for identification of isolates. Quarter-level culture results were used to establish cow-level IMI status at enrollment. Cows were followed from enrollment until 120 d in milk (DIM) in the subsequent lactation. Herd records were used to establish whether subjects experienced clinical mastitis or removal from the herd, and DHIA test-day data were used to record subclinical mastitis events (somatic cell count >200,000 cells/mL) and milk yield (kg/d) during the follow-up period. Cox regression and generalized estimating equations were used to evaluate the associations between IMI and the outcome of interest. The presence of late-lactation IMI caused by major pathogens was positively associated with postcalving clinical mastitis [hazard ratio = 1.5, 95% confidence interval (CI): 1.2, 2.0] and subclinical mastitis (risk ratio = 1.5, 95% CI: 1.3, 1.9). Species within the non-aureus Staphylococcus (NAS) group varied in their associations with postcalving udder health, with some species being associated with increases in clinical and subclinical mastitis in the subsequent lactation. Late-lactation IMI caused by Streptococcus and Streptococcus (Strep)-like organisms, other than Aerococcus spp. (i.e., Enterococcus, Lactococcus, and Streptococcus spp.) were associated with increases in postcalving clinical and subclinical mastitis. Test-day milk yield from 1 to 120 DIM was lower (-0.9 kg, 95% CI: -1.6, -0.3) in late-lactation cows with any IMI compared with cows without IMI. No associations were detected between IMI in late lactation and risk for postcalving removal from the herd within the first 120 DIM. Effect estimates reported in this study may be less than the underlying quarter-level effect size for IMI at dry-off and postcalving clinical and subclinical mastitis, because of the use of late-lactation IMI as a proxy for IMI at dry-off and the use of cow-level exposure and outcome measurements. Furthermore, the large number of models run in this study (n = 94) increases the chance of identifying chance associations. Therefore, confirmatory studies should be conducted. We conclude that IMI in late lactation may increase risk of clinical and subclinical mastitis in the subsequent lactation. The relationship between IMI and postcalving health and productivity is likely to vary among pathogens, with Staphylococcus aureus, Streptococcus spp., Enterococcus spp., and Lactococcus spp. being the most important pathogens identified in the current study.

Longitudinal study of herd udder hygiene and its association with clinical mastitis in pasture-based dairy cows

The objectives of this exploratory study were to (1) describe the association between herd-level udder hygiene and clinical mastitis and (2) investigate how sample size and milking stage affect the accuracy and precision of herd udder hygiene assessments made at milking time. A prospective longitudinal study was conducted in a dairy herd in Northern Australia as part of a previously published clinical trial of premilking teat disinfection. Video footage from 35 afternoon milkings was used to conduct 12,544 udder hygiene scores from 504 cows during an 89-d period and measure udder hygiene of the herd (proportion of cows with udder hygiene ≥3 out of 4). Linear interpolation was used to estimate herd udder hygiene on the days that were not scored, such that a herd-level udder hygiene measure was available for all cow-days in the study. Clinical mastitis events occurring during the study period were detected and recorded by farm staff according to a standardized definition. The relationship between herd udder hygiene on each of 1, 2, and 3 d before each study day (d -1, -2, and -3, respectively) and clinical mastitis at the cow level on each study day (each in turn being set as d 0) was determined using multivariable generalized estimating equations (family = Poisson, link = log), with the unit of analysis being the cow-day, adjusting for potential confounders and the clustering within the data. In addition, sampling strategies were evaluated by simulating herd udder hygiene assessments using a subset of cows in the herd. Herd udder hygiene from d -1, -2, and -3 was positively associated with clinical mastitis on d 0 (incidence rate ratio = 1.4 per 10-point increase in the percentage of cows with poor udder hygiene). Sampling strategy simulation found that at least 80 cows needed to be scored to achieve sufficiently precise estimations of herd udder hygiene. Furthermore, cows scored later during milking were slightly more likely to have poor udder hygiene than those scored earlier (risk ratio = 1.02 for cows that were 10% later in the milking order). More research is needed to evaluate risk factors for poor udder hygiene and potential interventions in pasture-based dairy cows.

Randomized equivalence study comparing the efficacy of 2 commercial internal teat sealants in dairy cows

The use of an internal teat sealant (ITS) at dry-off has been repeatedly shown to improve udder health in the subsequent lactation. However, almost all ITS research conducted in North America has evaluated one product (Orbeseal, Zoetis, Parsippany, NJ). The objective of this study was to evaluate a new ITS product (Lockout, Boehringer-Ingelheim Animal Health, Duluth, GA), by comparing it directly to Orbeseal in a multi-site, randomized, positively controlled equivalence trial for health indicators during the dry period [quarter-level new intramammary infection (IMI) risk, IMI cure risk, and IMI risk at 1 to 13 d in milk, DIM] and during the first 100 DIM [clinical mastitis and culling or death risk and test-day milk somatic cell count (SCC) and milk yield]. At dry-off, cows were randomly allocated to be treated with Orbeseal or Lockout after blanket administration of a cloxacillin dry cow therapy product. Cows were then followed from dry-off until 100 DIM. Intramammary infection status at enrollment and at 1 to 13 DIM was determined using standard bacteriological methods, allowing for the measurement of IMI dynamics during the dry period (i.e., IMI cures and new IMI). The effect of ITS group on dry period IMI cure, dry period new IMI, and IMI risk at 1 to 13 DIM was determined using generalized linear mixed models (logistic). Marginal standardization was used to derive risk difference estimates. An equivalence hypothesis test was conducted to compare ITS groups for dry period new IMI risk (margin of equivalence was ±5% units). The effect of ITS group on clinical mastitis and culling or death was determined using Cox proportional hazards regression. The effect of ITS group on test-day SCC and milk yield was determined using linear mixed models. Final models indicated that measures of quarter-level IMI dynamics were similar between ITS groups (i.e., risk difference estimates and 95% confidence intervals all close to zero). Furthermore, Lockout was found to be equivalent to Orbeseal for dry period new IMI risk using an equivalence hypothesis test. Hazard ratio estimates for clinical mastitis and culling or death were close to 1 and differences in SCC and milk yield between ITS groups were close to 0, indicating negligible effects of ITS group on test-day SCC and milk yield. In most cases, these effect estimates were relatively precise (i.e., narrow 95% confidence intervals). We conclude that producers using blanket dry cow therapy could consider including Orbeseal or Lockout treatment in their programs.

Randomized controlled non-inferiority trial investigating the effect of 2 selective dry-cow therapy protocols on antibiotic use at dry-off and dry period intramammary infection dynamics

Selective dry-cow therapy (SDCT) could be used to reduce antibiotic use on commercial dairy farms in the United States but is not yet widely adopted, possibly due to concerns about the potential for negative effects on cow health. The objective of this study was to compare culture- and algorithm-guided SDCT programs with blanket dry-cow therapy (BDCT) in a multi-site, randomized, natural exposure, non-inferiority trial for the following quarter-level outcomes: antibiotic use at dry-off, dry period intramammary infection (IMI) cure risk, dry period new IMI risk, and IMI risk at 1 to 13 d in milk (DIM). Two days before planned dry-off, cows in each of 7 herds were randomly allocated to BDCT, culture-guided SDCT (cult-SDCT), or algorithm-guided SDCT (alg-SDCT). At dry-off, BDCT cows received an intramammary antibiotic (500 mg of ceftiofur hydrochloride) in all 4 quarters. Antibiotic treatments were selectively allocated to quarters of cult-SDCT cows by treating only quarters from which aseptically collected milk samples tested positive on the Minnesota Easy 4Cast plate (University of Minnesota, St. Paul, MN) after 30 to 40 h of incubation. For alg-SDCT cows, antibiotic treatments were selectively allocated at the cow level, with all quarters receiving antibiotic treatment if the cow had either a Dairy Herd Improvement Association test somatic cell count >200,000 cells/mL during the current lactation or 2 or more clinical mastitis cases during the current lactation. All quarters of all cows were treated with an internal teat sealant. Intramammary infection status at enrollment and at 1 to 13 DIM was determined using standard bacteriological methods. The effect of treatment group on dry period IMI cure, dry period new IMI, and IMI risk at 1 to 13 DIM was determined using generalized linear mixed models (logistic), with marginal standardization to derive risk difference (RD) estimates. Quarter-level antibiotic use at dry-off for each group was BDCT (100%), cult-SDCT (45%), and alg-SDCT (45%). The crude dry period IMI cure risk for all quarters was 87.5% (818/935), the crude dry period new IMI risk was 20.1% (764/3,794), and the prevalence of IMI at 1 to 13 DIM was 23% (961/4,173). Non-inferiority analysis indicated that culture- and algorithm-guided SDCT approaches performed at least as well as BDCT for dry period IMI cure risk. In addition, the final models indicated that the risks for each of the 3 IMI measures were similar between all 3 treatment groups (i.e., RD estimates and 95% confidence intervals all close to 0). These findings indicate that under the conditions of this trial, culture- and algorithm-guided SDCT can substantially reduce antibiotic use at dry-off without negatively affecting IMI dynamics.

Randomized controlled trial investigating the effect of 2 selective dry-cow therapy protocols on udder health and performance in the subsequent lactation

The objective of this study was to compare culture- and algorithm-guided selective dry-cow therapy (SDCT) programs with blanket dry-cow therapy (BDCT) in a multi-site, randomized, natural exposure clinical trial for the following cow-level outcomes: clinical mastitis, removal from the herd, and Dairy Herd Improvement Association (DHIA) test-day milk yield and SCC measures during the first 120 d in milk (DIM). Two days before planned dry-off, cows in each of 7 herds were randomly allocated to BDCT, culture-guided SDCT (cult-SDCT), or algorithm-guided SDCT (alg-SDCT). At dry-off, BDCT cows received an intramammary antibiotic (500 mg of ceftiofur hydrochloride) in all 4 quarters. Antibiotic treatments were selectively allocated to quarters of cult-SDCT cows by only treating quarters from which aseptically collected milk samples tested positive on a rapid culture system after 30 to 40 h of incubation. For alg-SDCT cows, antibiotic treatments were selectively allocated at the cow level, with all quarters receiving antibiotic treatment if the cow met at least one of the following criteria: (1) any DHIA test with a somatic cell count >200,000 cells/mL during the current lactation, and (2) ≥2 clinical mastitis cases during the current lactation. All quarters of all cows were treated with an internal teat sealant. Clinical mastitis and removal from the herd events (i.e., culling or death) and DHIA test-day data from dry-off to 120 DIM were extracted from herd records. Hazard ratios (HR) for the effect of treatment group on clinical mastitis and removal from the herd during 1 to 120 DIM were determined using Cox proportional hazards regression. The effects of treatment group on test-day log_e-transformed SCC and milk yield were determined using linear mixed models. Final models indicated that either SDCT program was unlikely to increase clinical mastitis risk (HR_{cult-SDCT/BDCT} = 0.82, 95% CI: 0.58, 1.15; HR_{alg-SDCT/BDCT} = 0.83, 95% CI: 0.63, 1.09) or test-day log_eSCC (cult-SDCT minus BDCT = 0.05, 95% CI: -0.09, 0.18; alg-SDCT minus BDCT = 0.07, 95% CI: -0.07, 0.21). Risk of removal from the herd and test-day milk yield were similar between treatment groups. Findings from this study indicate that culture- or algorithm-guided SDCT can be used at dry-off without negatively affecting cow health and performance in early lactation.

Evaluation of rapid culture, a predictive algorithm, esterase somatic cell count and lactate dehydrogenase to detect intramammary infection in quarters of dairy cows at dry-off

Our objective was to compare four tests to standard milk culture followed by MALDI-ToF in quarters of cows at dry-off. Cows (n = 432) were randomly selected from seven U.S. dairy herds already participating in a multi-site clinical trial in summer 2018. Aseptic foremilk samples were collected from quarters (n = 1728) two days prior to dry-off, and subjected to index and reference tests. The four index tests included rapid culture, a predictive algorithm, an esterase strip test measuring somatic cell count (SCC) and a cow-side lactate dehydrogenase (LDH) test. Rapid culture was performed by inoculating quarter milk samples onto a commercial rapid culture plate. Plates were evaluated by technicians after 30-40 h of incubation at 37 ± 2 °C. Quarters were classified as infected if any bacterial growth was observed. For the algorithm test method, all quarters were classified as infected if the cow met any of the following criteria: 1) any Dairy Herd Improvement Association (DHIA) test with a SCC > 200,000 cells / ml during the current lactation or 2) two or more clinical mastitis cases during the current lactation. Esterase-SCC and cow-side LDH tests involved adding milk to the test strip and reading for color changes. For esterase-SCC and cow-side LDH tests, low (≥250 cells / ml and ≥100 U / L) and high (≥500 cells / ml and ≥200 U / L) thresholds were used to classify quarters as infected or not. Composite samples (4 × 2 mL quarter-milk samples commingled) were also tested for rapid culture, esterase-SCC and cow-side LDH tests, such that if a composite sample was positive, then all quarters contributing to that sample were classified as infected. The reference test was traditional aerobic culture conducted in an accredited laboratory using MALDI-ToF for identification of isolates. Traditional culture was only conducted on quarter-milk samples, and consequently, IMI was always considered at the quarter-level. Unconditional logistic regression was used to estimate sensitivity (SE), specificity (SP), apparent prevalence, positive predictive values (PPV) and negative predictive values (NPV) for each index test. Cohen's Kappa (κ) was used to measure agreement between tests. Algorithm, esterase-SCC and cow-side LDH tests had poor agreement with the reference test (κ ranging from 0.01 to 0.12), while rapid culture had fair agreement (κ = 0.28). No test had concurrently high SE and SP. Negative predictive values were moderate to high for all tests.

Cross-sectional study of the relationship between cloth udder towel management, towel bacteria counts, and intramammary infection in late-lactation dairy cows

Because cloth udder towels (CUT) may function as a fomite for mastitis-causing pathogens, most udder health laboratories offer towel culture services as a tool to monitor towel hygiene. However, no studies have investigated if an association exists between bacteria levels in CUT and udder health outcomes. The objectives of this cross-sectional study were to (1) describe associations between herd-level measures of towel bacteria count (ToBC) and quarter-level intramammary infection (IMI) status in late-lactation cows, (2) establish pathogen-specific target levels of bacteria in CUT to aid the interpretation of towel culture reports, and (3) identify laundering-related risk factors for high ToBC. The study was conducted in 67 herds from 10 dairy states in the United States that used CUT. These 67 herds were originally recruited as part of a larger (80 herd) cross-sectional study of bedding management. Each herd was visited once during December 2017 to April 2018 and quarter-milk samples (n = 4,656) were collected from late-gestation (>180 d pregnant) cows (n = 1,313). Two recently laundered CUT were collected and a questionnaire was used to collect information about pre-milking teat preparation and CUT management practices. Quarter-level IMI status was determined using standard bacteriologic methods. In addition, colony-forming units of all bacteria (total bacteria), Staphylococcus spp., Streptococcus spp. or Streptococcus-like organisms (SSLO), coliforms, noncoliform gram-negatives, and Bacillus spp. were determined for each pair of CUT (log₁₀ cfu/cm²). The association between ToBC and IMI was determined using multivariable logistic regression with mixed effects. After dichotomizing ToBC into high and low categories, associations between towel management practices and ToBC category were determined using unconditional logistic regression. The quarter-level prevalence of IMI was 19.6%, which was predominantly caused by non-aureus Staphylococcus spp. (NAS; 10.2%) and SSLO (5.1%). The predominant bacteria in CUT were Bacillus spp. (median = 3.13 log₁₀ cfu/cm²). Total bacteria count was not associated with odds of IMI (odds ratio = 1.06), likely due to the predominance of Bacillus spp. in CUT and low number of IMI caused by Bacillus spp. In contrast, counts of Staphylococcus spp. and SSLO were positively associated with odds of IMI caused by NAS (odds ratio = 1.33) and SSLO (odds ratio = 1.45), respectively. Of 12 CUT management practices evaluated, only the failure to use a dryer was identified as a clear predictor of risk for a high ToBC (risk ratio of high coliform count = 8.17). Our study findings suggest that CUT may act as a fomite for NAS and SSLO. We recommend that herds aim to keep counts of Staphylococcus spp. and SSLO in CUT below 32 cfu/cm² (or 5 cfu/in²), and that laundered towels be completely dried in a hot air dryer.