4.4 Scenario: Pneumonia on a Small Midwest Organic Dairy Farm

Katie Steneroden

To better understand the treatments highlighted in this scenario, we highly recommend completing the Rules and Regulations chapter beforehand and referencing the handout, Guidance for treating organic and alternative animals.

Knowledge reviews are included in this section. Please read through the questions and think about how you would answer the question. Answers are provided at the end of the chapter.

You are called out to an organic dairy farm in Wisconsin in late March for an acute death in a 3-month-old heifer. Another calf is lethargic, didn’t finish its milk this morning, and is coughing. The weather has been severe, with a warm period followed by cold temperatures and wet, slushy snow.

Jay Snyder owns Pine Bluff Farm. His farm has been certified organic for the past four years. The farm has 60 milking cows, six milk-fed calves, and 20 heifers.

This time of year, the cows are in a tie-stall barn with a concrete loafing area used for turn-out. The heifers are in a bedded pack pen built as an addition to the main tie-stall barn and share air space with it. The milk-fed calves are in box stalls at the end of the barn closest to the milk house to be checked on and fed easily.

Day 1

On examination, you find a 2-month-old heifer calf in good body condition with slight nasal discharge and mildly depressed. The calf is alert and gives you a bit of a run to catch and examine it. The temperature is 104.5°F. The respiratory rate is 60 bpm, and the lungs are a little harsh ventrally. The calf coughs a few times during the exam.

Knowledge Review 1

Organic cattle with infections exhibiting mile to moderate clinical signs (detected early in the course of the disease) can often be treated without antibiotics using supportive care, supplements, and natural remedies. Which of the following actions would NOT be recommended for mild infection?

  1. Managing the environment by improving ventilation and providing deep, clean, dry bedding.
  2. Adding supplements to the ration (i.e. increased vitamin levels [or probiotics]) and using an anti-inflammatory to manage fever and improve appetite.
  3. Wait to see if the animal’s immune system responds appropriately before treating.
  4. Treatment with herbal (botanical) preparations having biological activity.
  5. Rechecking the animal frequently for response to treatment and switching to an antibiotic if signs deteriorate

Next, you perform a postmortem exam on the dead heifer calf. Jay’s son—who feeds the calves—didn’t notice anything unusual about the calf yesterday and was surprised to find it dead this morning.

On examination, you find a 3-month-old calf in good body condition with slight purulent nasal discharge. Internally, you find severely congested, darkened lung tissue in the cranioventral lobes. A piece of lung tissue from the consolidated area sinks when placed in your wash bucket. Tissue from the more normal-looking dorsal lobes floats. There is an increased amount of pleural fluid in the chest cavity. Purulent discharge is present in the upper respiratory system. All else is normal.

You explain to Jay that the dead calf had an acute case of pneumonia, and the sick calf also has a respiratory infection that needs treatment. Jay thanks you for the diagnosis but declines to give antibiotics to the sick calf and treats her orally with an herbal, garlic-containing tincture.

Knowledge Review 2

When considering treatment options for respiratory disease on an organic dairy cow farm, which list below includes three prohibited substances that would permanently disqualify treated animals from organic production:

  1. Naxel, flunixin meglumine, dexamethasone
  2. Dexamethasone, antihistamine, aspirin
  3. Ceftiofur, dexamethasone, Vitamin C
  4. Penicillin, dexamethasone, tripelennamine HCL

You administer a dose of Flunixin IV to the sick calf. You also give the calf an injection of Amplimune® and bovine antiserum for immune support. Since the herd has not been vaccinated for respiratory viruses, you recommend vaccination of the herd with a live intranasal vaccine, but Jay declines.

Day 2

Jay calls back to report another sick calf and two coughing cows near the milk-fed calf stalls that didn’t finish their feed this morning. The heifer calf treated yesterday has improved and drank its milk well.

You examine the two cows (Emma and Mocha) and find temperatures of 104-105°F, increased respiration rates, and mild to moderate lung sounds indicating early pneumonia. You recommend antibiotic treatment, but Jay declines as he wishes to treat the cows with herbal tincture and supportive care. In addition to Jay’s treatment, you give the cows IV flunixin and vitamin C. The cows also get a dose of bovine antiserum (Bovi-Sera, or Multi-Serum), SQ.

The five-month-old bull calf exhibits moderate respiratory signs on examination, similar to the cows. Jay explains he recently bought the bull calf from a neighboring organic dairy ten days ago and plans to raise him as the herd bull.

You treat the bull calf with a broad-spectrum antibiotic and flunixin. Jay doesn’t hesitate to use antibiotics in this animal since a herd bull doesn’t need to be certified organic. The bull will lose its organic status as a meat animal but can still be used as a breeding animal after treatment. The bull will need to be sold to a conventional market in the end.

You have another discussion with Jay regarding vaccination and ask him about his concerns. Jay has not vaccinated his livestock since going organic and has not had any problems until now, but they have experienced greater weather challenges this year. You agree that it has been an especially rough winter and mention that another organic farm you work with used the respiratory vaccine and has not had issues with respiratory disease this year. Jay agrees this might be a good year to vaccinate the herd.

You and Jay vaccinate the cows in tie stalls with an intranasal vaccine. You dispense additional doses of intranasal vaccine for the heifers and calves—Jay and his son will vaccinate them later that day.

Day 3

You return the following morning to assess the situation and address the herd’s needs. The original sick cow, Mocha, and the bull calf are all doing better. Jay will continue herbal treatment and supportive care for these individuals for another 2 or 3 days. Emma (the second cow) is no better and has gotten slightly worse—mostly off feed, respiration rate, effort, and lung sounds have all increased, but she still nibbles at her feed and isn’t in severe respiratory distress.

There are no new cases today, but Jay is very concerned about Emma. He tells you he has previously waited too long to use antibiotics and regretted it. You tell Jay that you believe antibiotics are necessary at this point with this cow, and he agrees. You treat Emma with antibiotics since she didn’t respond to organic treatment. You use an antibiotic with a relatively short withdrawal time (Ceftiofur) and advise Jay that he will need to report the use of a prohibited substance to his certifier, segregate Emma, and dump her milk until the withdrawal time has passed. When practical, he can market her through a conventional channel to another farm or for conventional processing.

Knowledge Review 3

True or false: Animal health providers must refer to the NOP list of allowed synthetics (CFR 205) to determine specific organic withdrawal times for each specific drug as they differ from the withdrawal times listed on the label.

  1. True
  2. False

Day 4

Jay calls your office the next morning and speaks with the receptionist. Jay reports Emma has responded well to antibiotic treatment. The other cattle are improving, and Jay doesn’t feel you need to recheck them. Jay requests flunixin and vitamin C prescriptions through an online livestock supplier he buys from. The receptionist relays the message from Jay to you.

You return Jay’s call between farm calls. “I’m delighted to hear that your cows are doing well! I see you are requesting some prescription medications. To fill those prescriptions, I would need to be your veterinarian of record. What that comes down to is that we would have to establish a veterinary-client-patient relationship, a VCPR.  It would entail regular visits to your farm to make sure I am up on all your animal care practices and review your animal health records. We would agree to open communication on the health needs of your animals, and I would also be available to follow up on issues you experience with your livestock. I would be happy to discuss the details if you are interested”. Jay says he is interested, and you set up a farm visit to discuss the details and establish the VCPR.

Knowledge Review 4

If an organic farmer wishes to use—or keep in inventory—any prescription medication on the NOP National List of Allowed Synthetic Materials, which of the following requirements must be met?

  1. The drug must be specifically listed as allowed in the Code of Federal Regulations 205.603; synthetic substances allowed for use in organic livestock production.
  2. A licensed veterinarian must oversee the prescription and use of the drug(s)
  3. A valid VCPR must exist between the farmer and a licensed veterinarian who prescribes or supplies the allowed substance.
  4. Records of use, including the treated individual animal’s ID, dates, dose(s) administered, and specific withdrawal times, must be recorded and kept.
  5. All. Of the above
Knowledge Review 5

What potential veterinary services could be beneficial to organic livestock producers?

  1. Consultation to update the herd health plan concerning biosecurity practices
  2. Follow-up herd vaccination procedures and reminders to vaccinate
  3. Prescription writing with the context of a valid VCPR
  4. Evaluation of housing facilities regarding ventilation
  5. Assistance with record keeping of morbidities, mortalities and treatments
  6. All of the above

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Organic and Alternative Livestock Health Copyright © 2026 by Katie Steneroden; Jenna Bjork; and Delaine Quaresma is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License, except where otherwise noted.

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