Necropsy results for 11 week old chick


Sep 11, 2019
Hello everyone,
This is me and my husbands first flock of chickens and I think we have started off on a very wrong foot. We got several chicks from various breeders around the same time and did not keep them separate, which I now realize was a mistake. About 2 weeks later a few (3 of 10) started showing respiratory illness symptoms. I took one to the vet and the vet just gave her some antibiotics and did not do any testing. I put antibiotics in the water, and finally moved them out of the brooder and into their new coop a few weeks after that. All the respiratory symptoms were gone.

We had a very underweight 11-12 week old chick die recently and we sent her for a necropsy at the state lab and I'd like some help understanding the necropsy and whether or not I should use these findings to treat the rest of the flock for anything. Obviously the resp. issues were mycoplasma s., so I am mostly confused about the e. coli. Is this something the rest of the flock has and I need to treat? The rest seem healthy, active and they are eating and drinking. The poor thing I sent in for the necropsy had all sorts of issues. She was weak on one side and had lice. One of the tests came back for coccidiosis, but i treated the flock twice in the water with Corid prior to her death. Is it safe to assume her water intake was reduced and she didn't get the full dose? Also what is "mixed flora"?

The absolute worst part is that I have several surprise roosters and now I don't know what to do with them. I was planning on giving them to other people but with m.s. in the flock that wouldn't be good. I am not allowed to keep them and one just started crowing this morning. I am so bummed that we may have to cull chickens we raised. This was certainly not the "plan" when we started. Has anyone had luck giving roosters to people and disclosing M.S.and is it possible the roosters don't have it, and is there a particular test I could ask the vet to do to check (would it even be worth).

My apologies for the bad formatting below.

Coccidiosis, enteric
Mycoplasma synoviae positive

Diagnosis Comment
This young bird had multiple organs infected with E. coli bacteria, and had coccidia in the fecal flotation. PCR testing was
positive for Mycoplasma synoviae but negative for Avian influenza.
Lab Findings

Specimen Test Name Organism Drug MIC Interpretation
Meyer - Avian - Galliform / poultry - Chicken - 2 Months
Escherichia coli -1

Antibiotic Susceptibility - 9/9/2019 10:34 AM Escherichia coli

Amoxicillin 4 Susceptible
Ceftiofur 0.5 No Interpretation
Clindamycin >4 Resistant
Enrofloxacin <=0.12 No Interpretation
Erythromycin >4 No Interpretation
Florfenicol 4 Intermediate
Neomycin <= 2 Susceptible
Novobiocin >4 Resistant
Oxytetracycline >8 Resistant
Penicillin >8 Resistant
Spectinomycin 64 Resistant
Streptomycin 32 Resistant
Sulphadimethoxine >256 Resistant
Sulphathiazole >256 Resistant
Tetracycline >8 Resistant
Sulfamethoxazole <= 0.5 Susceptible
Tylosin (Tartrate/ Base) >20 No

Specimen Test Name Organism Growth Amount
Meyer - Avian - Galliform / poultry - Chicken - 2 Months
Trachea - Tissue, fresh - 1 Bacterial Unknown ID (Aerobic Culture) - 9/9/2019 10:34 AM Mixed Flora Heavy
Yolk Sac - Tissue, fresh - 2 Bacterial Unknown ID (Aerobic Culture) - 9/6/2019 10:50 AM Escherichia coli Heavy
Spleen - Tissue, fresh - 3 Bacterial Unknown ID (Aerobic Culture) - 9/6/2019 10:50 AM Escherichia coli Heavy

Specimen Test Name Result
Avian - Galliform / poultry - Chicken - 2 Months
Intestine - Tissue, fresh - 4 Salmonella (Culture) - 9/9/2019 10:34 AM Not detected

In vitro susceptibility test results may not correspond with in vivo conditions.
Veterinary-specific interpretive criteria may be unavailable for some antibiotics listed. Not all drugs listed
are approved for use in food-producing animals and may not be species specific. Consult with your
veterinarian concerning dosage and withdrawal times. The laboratory assumes no responsibility for
efficacy, safety or residue avoidance in the use of these antibiotics.
The in vitro susceptibility of microorganisms to antibiotics is established by the Clinical Laboratory
Standards Institute (CLSI). In some cases, the microorganism-antibiotic combination has not yet been
validated by CLSI, and the result is reported as No Interpretation (NI). This does not mean that the
microorganism is not susceptible to the antibiotic; the antibiotic may still be useful for treatment by
considering pharmacokinetics, toxicity and host factors.

Molecular Testing
Specimen Test Name Type A Matrix H7 Primers H5 Primers
Meyer - Avian - Galliform / poultry - Chicken - 2 Months
Trachea - Swab - 7 Avian Influenza (AI) (PCR) - 9/6/2019 3:13 PM Negative 0.00 No Test 0.00 No Test 0.00

Specimen Test Name MS RRT-PCR
- Avian - Galliform / poultry - Chicken - 2 Months
Trachea - Swab - 7 Mycoplasma (MS RRT-PCR) - 9/6/2019 3:13 PM Positive

Specimen Test Name MG RRT-PCR
- Avian - Galliform / poultry - Chicken - 2 Months
Trachea - Swab - 7 Mycoplasma - 9/6/2019 3:13 PM Negative

Specimen Test Name Parasite Parasite Amount
Meyer - Avian - Galliform / poultry - Chicken - 2 Months
Intestine - Feces - 5 Parasite Unknown ID (Fecal Floatation Sugar) - 9/5/2019 3:03


No Parasites Detected -Sample collected by client

Intestine - Feces - 6 Parasite Unknown ID (Fecal Floatation Sugar) - 9/5/2019 3:03PM
Coccidia Moderate parasite load -Collected during necropsy

Thanks for your help! This has been emotionally exhausting :(
You're feeling overwhelmed because this is overwhelming for anyone to have to deal with. You've also had a slap across your face for your choices made while starting your flock from private breeders. Try not to feel badly. Many of us, myself included, made the same mistake when starting our flocks, and now we are dealing with a chronic avian disease in our flocks.

The chick you had necropsied did indeed have a lot going against it. The CRD is now in all of the chickens in your flock. It will crop up from time to time if stress factors come into play. Then you will treat the chickens that are showing the symptoms. There isn't anything else to do in that area until you notice a sick chicken.

The E-coli and coccidiosis are things that attack a chicken with a very weak immune system. Healthy chickens usually fight these off with little to no problems. It wouldn't hurt, though, to give your remaining flock a course of Corid to be safe.
I am not an expert on respiratory disease, but these links may help. This will also bump your post, so hopefully some more people will weigh in.
Since you have a positive test for Mycoplasma synoviae, then that is probably your biggest issue. It's very contagious, and it's chronic. E coli often affects birds that have respiratory infections. For both, sanitation is important to help prevent the spread, especially of waterers. Birds weakened with other things become more susceptible to coccidiosis also. Exposure to the coccidia usually allows them to build some resistance and healthy birds won't get sick, but with a weakened immune system, they don't have the ability to fight it.
Hopefully these links will provide some helpful info:
I just want to say that your start to chicken keeping sounds a bit like my own. I lost two early on to unknown illness and maybe didn't do everything by the books and felt it was all my fault. I had sleepless nights of monitoring the coop temperature in snow storms and giving meds and water by syringe every two hours and I wondered if I had made a terrible mistake and if I was cut out for chicken keeping. It is not all snuggling cute little fluffy chicks by any means. I just want to tell you that it gets easier. I promise. Once your flock is established, daily care and maintenance is a breeze. Routine cleaning is spaced out much more than brooder cleaning. A bit of feed and water once a day is generally all the attention they need and you will be free to sit back and enjoy their antics and companionship, or to just go about the rest of your life without constantly worrying about them. The stress level will go down and the enjoyment will go up. It does take a bit of time to get to this point, especially when you are new, and especially when you are dealing with illness in the flock, but I promise, it gets easier and it gets better and they will no longer be a source of stress. :hugs
Thank you all for the information and support. I feel like the flock is doing ok right now. No obvious symptoms of distress from any of the chicks. No bloody poops and no respiratory illness symptoms. No one is lethargic. I've treated them for lice with permethrin 2x, I forgot to mention the chick that died also had body lice. Ugh.

I did the full outbreak treatment for cocci with Corid, twice before the chick died. Should I do it again or just monitor them for symptoms?
unfortunately no, it is highly contagious, your flock needs to remain closed no birds or eggs in or out and extremely strict bio security, or culled they will always carry it. Do not have an idea what you would have to do to clean up after that though, I am so sorry you have had such a rough start.
Tagging some people that can better advise you

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