Frequently, when we talk about high quality forages and TMR, we focus on the nutritional aspects: digestibility, crude protein, starch, etc. However, an aspect that is often overlooked, and is just as important as the nutrient content of a diet, is the anti-nutritional components and their potential impact on health and productivity. Anti-nutritional factors are substances that, when present in animal feed or water, either directly or indirectly through their metabolic products reduce the availability of one or more nutrients (Yacout, 2016). When focusing on hygiene of forage or TMR, the anti-nutritional factors that would draw the most intense scrutiny would be the pathogenic microorganisms and toxins. The most common pathogenic microorganisms found in poorly fermented silage are Escherichia coli, specifically E. coli 0157:H7, Listeria monocytogenes, Bacillus spp., Salmonella and Clostridium spp. (Wilkinson, 1999). Forages can be contaminated with pathogens during one of four points: prior to harvest (manure/compost application to fields), during harvest (contaminated with soil-borne pathogens), silage fermentation (inadequate or sub-optimal) and during feed-out (poor aerobic stability leading to opportunistic pathogen growth). The impact of contamination at any of these times, can be detrimental to animal health, productivity and overall profitability. Presence of pathogenic microorganisms in silage may lead to digestive upset, enteric disease, poor animal performance and potentially death.




Enterobacteriaceae is the family of Gram-negative bacteria, that includes over 51 genera and 238 species encompassing beneficial commensal microbiota and opportunistic pathogens (Octavia and Lan, 2014).Members of the Enterobacteriaceae family include Salmonella, E. coli, Listeria, Shigella and Klebsiella, to name a few. These bacteria are widely distributed in nature, and many species live in the G.I. tract of humans and animals. Unfortunately, some of these bacteria, specifically Salmonella and E.coli are pathogenic and can cause acute enteric disease in both cattle and humans.


There are two recognized species within the Salmonella genus: Salmonella enterica and Salmonella bongori. Salmonella enterica can be further divided into 6 subspecies, with Salmonella enterica subspecies enterica being the most relevant in dairy cattle (Smith, 2009). More than 2,500 serovars or serotypes, differentiated by their antigenic composition, have been identified. Serovars are based on the somatic (O), flagellar (H), and capsular (Vi) antigens
(Bopp et al., 2003). Clinical bovine isolates have been divided by their O antigens, and serovars are further grouped into serogroups assigned to a letter of the alphabet (A, B, C, D, and E; Peek et al., 2017). Salmonella isolates are referred to by their serovar/serogroup classification (ex, Salmonella enterica subspecies enterica serovar Typhimurium, is abbreviated to Salmonella Typhimurium).


Despite the diversity of serovars, relatively few are of clinical importance in cattle, these include: Salmonella Typhimurium, S. Newport, S. Cerro and S. Dublin. The majority of cattle isolates are Salmonella of Types B, C, and E, which are non–host specific, or Salmonella Dublin (Type D), which is the host-adapted serovar in cattle (Peek et al., 2017). Salmonella is most commonly transmitted by fecal-oral contamination from other livestock, rodents, birds or contaminated feed (Smith, 2009). Factors that determine the pathogenicity include virulence of serotype, dose of inoculum, degree of immunity, previous exposure and other stressors currently affecting the host (Mohler et al., 2009). Once ingested, Salmonella attach to mucosal cells and are capable of destroying enterocytes. Attachment is increased if gastrointestinal stasis is present or normal flora has been disturbed or is not yet established (Smith, 2009).



Enteric, septicemic and reproductive diseases are all possible manifestations of Salmonella infections (Holschback and Peek, 2018). During the early stages of the acute enteric disease, affected animals develop fever, dullness, loss of appetite, depressed milk yield and adult pregnant animals may abort. Pneumonia is an increasingly common manifestation of Salmonella Dublin in calves (Pecorara et al., 2017). 



Dairy cows may serve as asymptomatic carriers of Salmonella, thus allowing Salmonella to go undetected until there is an outbreak. The potential for herd carrier status increases with herd size, and Salmonella shedding may be triggered by stress placed on the animals. Salmonella is commonly isolated from the feces of animals that do not show symptoms of salmonellosis. In one study (Van Kessel et al., 2008), Salmonella was isolated from 8% of asymptomatic cattle. In another study in the US, 27–31% of dairy farms were found to have cows that shed Salmonella; on these farms between 5.4 to 7.3% of the cattle were found to shed Salmonella (USDA/APHIS, 2003). Detecting the presence of Salmonella in a herd, prior to an outbreak, allows the producer to manage mitigation of the pathogen, and reduce the risk of a future outbreak.




Escherichia coli, more commonly known as E. coli, is a well-known, organism and ubiquitous in nature. While some E. coli is non-pathogenic and part of the normal intestinal microbiota of many animals, Shiga-toxin-producing E. colii (STEC) is pathogenic and a human health concern, primarily as a food-borne pathogen. The majority of cases of STEC infection in humans have been associated with serotype O157:H7, but STEC serogroups O26, O103, O111, and O145 are also significant causes of human diseases (Gould et al., 2013). Although STEC does not cause enteric disease in cattle—because cattle do not possess Shigatoxin receptors — it’s important to monitor in cattle due to the food safety and human health concerns.



Clostridia, members of the Clostridiaceae family, are an important component when talking about feed hygiene and GI health. Clostridium are gram-positive, anaerobic, spore-forming bacteria that are often found in the soil and manure or in feedstuffs that have been contaminated. Clostridium perfringens can cause a range of diseases with the main concern in lactating cattle being enteric diseases that affect the GI tract. C. perfringens is classified into five Types, A to E, depending on the production of four major toxins (alpha, beta, epsilon, and iota; Fohler et al., 2016). C. perfringens becomes pathogenic when stressors increase (feed change, too much starch, pen changes, etc.), and the GI tract creates favorable conditions for proliferation. When elevated levels of the toxins released by C. perfringens enter the bloodstream animals can experience inflammation, shock, cardiac arrest and even death.




Evaluating TMR and manure for Enterobacteriaceae and Clostridium provide us with valuable information to have a conversation around both forage inoculants as well as probiotics. Initial efforts by the Chr. Hansen team to quantify and describe hygiene metrics on-farm focused on forages and their impacts on the overall TMR quality and aerobic stability in the feed bunk. Sample analyses and subsequent discussions with dairy owners and managers resulted in adoption of, and stricter adherence to, the Critical Control Points (CCP) for harvest, storage and feed-out, and increased use of SILOSOLVE® silage inoculants. 


Subsequently, this effort extended beyond ensiled forages and the Chr. Hansen inoculant portfolio. A comprehensive hygiene analysis on-farm can be conducted for TMR and water samples, and for quantification of pathogen load in composite manure samples. The TMR and water samples provide a perspective of what the cows may be consuming, while the composite manure samples serve as an indication of the overall GI tract health of cows. Composite manure samples are more sensitive than individual or pooled samples due to the number of cattle being indirectly sampled (Lombard et al., 2012). This extension of hygiene analysis and resulting metrics has enhanced the conversation around forage quality and inoculants, but at the same time, elevated the importance of feeding a science-based, research-proven probiotic to every animal, every day. The discussion ultimately culminates with how maintaining a normal GI tract, and normal microbiota significantly reduces the risk of enteric disease and clinical outbreaks. These analyses and, more importantly, the presentation of the resulting metrics, allow Chr. Hansen team members to have discussions with not only the herd owner or manager, but also the nutritionist and consulting veterinarian.


Комплексна гігієна - ПМР, Гній, Вода

Initial samples (TMR, water and composite manure) should be collected 1 to 7 days prior to feeding a Chr. Hansen probiotic, with follow-up sampling (composite manure) occurring between 30 to 45 days. Additional samples can also be collected at 90 and 180 days but are not required. Results are entered into a visual metric that easily highlights where the sample falls within the excellent, good, average, fair or poor classifications. The TMR metric includes yeast, mold, C. perfringens Type A, Enterobacteria, Vomitoxin, Zearalenone, Aflatoxin and T-2 (Fig. 1a). The water metric includes enumeration of coliforms and E. coli (Fig. 1b), while the composite manure metric includes E. coli STEC, Salmonella sp., Clostridium perfringens, and Clostridium perfringens Type A (Fig 1c).


  Results from subsequent manure samples can be compared to previously obtained samples to evaluate if shedding rates have decreased while on the probiotic. Decreases in E. coli STEC, Salmonella sp., Clostridium perfringens and Clostridium perfringens Type A are indicative of improved GI health due to feeding the probiotic. For answers to your questions and to see how Composite Hygiene Metrics could benefit your dairy, reach out to your regional Chr. Hansen Technical Service Specialist for more information.




Bopp CA, Brenner FW, Fields PI, et al. Escherichia, shigella, and salmonella. In: Murray PR, Baron EJ, Jorgensen JH, et al, editors. Manual of clinical microbiology, vol. 1, 8th edition. Washington, DC: ASM Press; 2003. p. 654–71. 


Callaway TR, Keen JE, Edrington TS, Baumgard LH, Spicer L, Fonda ES, Griswold KE, Overton TR, VanAmburgh ME, Anderson RC, Genovese KJ, Poole TL, Harvey RB, Nisbet DJ. Fecal prevalence and diversity of Salmonella species in lactating dairy cattle in four states. J Dairy Sci. 2005 Oct;88(10):3603-8. 


Fohler S, Klein G, Hoedemaker M, et al. 2016. Diversity of Clostridium perfringens toxin-genotypes from dairy farms. BMC Microbiol. 2016;16(1):199. doi:10.1186/s12866-016- 0812-6 


Gould, L. H., R. K. Mody, K. L. Ong, P. Clogher, A. B. Cronquist, K. N. Garman, S. Lathrop, C. Medus, N. L. Spina, T. H. Webb, P. L. White, K. Wymore, R. E. Gierke, B. E. Mahon, and P. M. Griffin. 2013. Emerging Infections Program Foodnet Working Group. Increased recognition of non-O157 Shiga toxin–producing Escherichia coli infections in the United States during 2000–2010: Epidemiologic features and comparison with E. coli O157 infections. 10:453–460. 


Hoschback, C.L. and S.F. Peek. 2018. Salmonella in dairy cattle. Vet. Clin. Food Anim. 34:133–154 https://doi. org/10.1016/j.cvfa.2017.10.005 


Lombard JE, Beam AL, Nifong EM, et al. Comparison of individual, pooled, and composite fecal sampling methods for detection of Salmonella on U.S. dairy operations. J Food Prot 2012;75(9):1562–71. 


Mohler VL, Izzo MM, House JK. Salmonella in calves. Vet Clin North Am Food Anim Pract 2009;25(1):37–54. 


Octavia S., Lan R. (2014) The Family Enterobacteriaceae. In: Rosenberg E., DeLong E.F., Lory S., Stackebrandt E., Thompson F. (eds) The Prokaryotes. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-38922- 1_167 


Pecoraro HL, Thompson B, Duhamel GE. Histopathology case definition of naturally acquired Salmonella enterica serovar Dublin infection in young Holstein cattle in the northeastern United States. J Vet Diagn Invest 2017. 


Peek SF, Cummings KJ, McGuirk SM, et al. Infectious diseases of the gastrointestinal tract. In: Peek SF, Divers TJ, editors. Diseases of dairy cattle. 3rd edition. St. Louis(MO): Elsevier; 2017.  


Smith BP. Salmonellosis in ruminants. In: Smith BP, editor. Large animal internal medicine. 4th edition. St. Louis(MO): Mosby; 2009. p. 877–81. 


U.S. Department of Agriculture. 2003. Part III: Reference of dairy cattle health and health management practices in the United States, 2002. National Animal Health Monitoring System, U.S. Department of Agriculture, Animal and Plant 


Health Inspection Service, Veterinary Services, Centers for Epidemiology and Animal Health, Washington, D.C. 


Van Kessel, J.S., Karns, J.S., Wolfgang, D.R., Hovingh, E., Jayarao, B.M., Van Tassell, C.P., Schukken, Y.H. 2008. Environmental sampling to predict fecal prevalence of Salmonella in an intensively monitored dairy herd. J. of Food Prot. 71(10):1967-1973. 


Wilkinson, J. M. 1999. Silage and health. Pages 67–81 in Silage production in relation to animal performance, animal health, meat and milk quality. Proceedings of the 12th International Silage Conference, July 5–7, Uppsala, Sweden. T. Pauly, ed. Swedish University of Agricultural Sciences, Uppsala, Sweden.


 Yacout M.H.M. 2016. Anti-nutritional factors & its roles in animal nutrition. J, Dairy Vet, Anim, Res. 4(1):237-239. DOI: 10.15406/jdvar.2016.04.00107.