How do chickens get Salmonella, anyway?

Andrea Etter

I don’t think I’ve done a post on this before, so here goes… Ever wonder where chickens get Salmonella from? It turns out there are a lot of options. In our research it seems adults most likely get Salmonella from the environment, feed, wild animals/birds, or each other (yes, feed can contain Salmonella–probably from birds/mice/other animals pooping in it). Chicks, however, often arrive from hatcheries already infected, which may mean they are born infected with it (option A). Either way, it can get you sick. Fortunately, research on commercial birds indicates that many/most infected chicks clear Salmonella by adulthood.

Ways chickens can get Salmonella

What we found in 2022: baby chicks

2022 was our third year of agricultural supply store sampling for Salmonella. We sampled at 9 stores across Vermont, collecting a total of 195 samples from March-July 2022.

So, what did we find?

Overall positivity rates were slightly higher this year (40.5% vs 34%). Hatcheries not participating in NPIP Salmonella monitoring programs had higher rates of Salmonella in 2022 than 2021, but we added a new hatchery for that category this year and had more samples overall in the non-NPIP category. Hatcheries participating in Salmonella monitoring programs had roughly the same rate of Salmonella as in 2021.

Breaking out the data by hatchery, you can see that there are differences in Salmonella rates between hatcheries, you can see that Hoovers hatchery has the highest rates of Salmonella, while Townline had the lowest. NOTES: We only have one year of data for Ridgeway, so that rate may change as we get more years of data and samples. Hoovers store A had the lowest biosecurity, which may explain the high rates of Salmonella, but Store B still had higher rates of Salmonella than any other store.


  • Salmonella is super common in baby chicks sold to hobby poultry enthusiasts
  • Hatchery participation in the NPIP Salmonella monitoring program does not improve Salmonella rates in chicks
  • You should assume baby chicks have Salmonella and take precautions
    • Don’t let kids put chicks near their face. Chicks are messy and will have poop on their legs and possibly feathers
    • If you let kids pet the chicks (which is ok), make sure they wash their hands thoroughly afterwards
    • Don’t put chicks in the kitchen; dust can contain fecal particles.
      • The best place for chicks is a basement, warm garage, or unused bathroom–something that isn’t in the main part of the house and harder for any small children to access.
    • Don’t wash chick water containers or feed containers in the kitchen sink. A bathtub or utility sink is better

Dr. Etter

We’re still doing research!

Rooster on a post

We have been busy processing samples this summer and going through the review process with our first paper from this project, but we’re looking forward to gathering some more backyard flock samples in August and September. Interested in participating? Check out the options here.

We will be at the International Association for Food Protection July 31-August 3rd, presenting our research from 2021 on chicks from agricultural supply stores. Our abstract is below:

IAFP 2022 abstract

Curious about the adult side of the project? Our project abstract is below, and you can find the preprint on ResearchGate.

The popularity of backyard chickens has been growing steadily over the past ten years, with Covid-19 stay at home orders in 2020 providing an added boost in popularity. Concurrently, cases of salmonellosis from live poultry exposure have also risen. Previous research on backyard chicken owners has focused primarily on urban chicken owners, which may have differing knowledge and biosecurity habits from rural backyard chicken owners. The goal of this study was to investigate the prevalence of S. enterica in rural and urban flocks of chickens in the state of Vermont and to determine what attitudes towards and knowledge about S. enterica owners had, as well as what biosecurity practices they used. We conducted two surveys in Vermont between 2019-2022; a pilot study tied to sampling for Salmonella enterica in backyard chicken flocks from 2019-2021 and a statewide study in 2022 to determine the prevalence of backyard chickens in Vermont and obtain representative survey data from backyard chicken owners. We found (i) overall, 19% (8/42) backyard chicken flocks from 2019-2021 had S. enterica, but S. enterica rates varied substantially by year; (ii) backyard chicken owners were wealthier and more educated than the average Vermonter and generally lived in rural areas; (iii) participants in the statewide survey had much lower uptake of good biosecurity habits compared to the pilot survey; (iv) despite increased messaging about backyard chicken-associated salmonellosis and good biosecurity measures over the past several years, uptake of biosecurity measures is inconsistent, and rates of unsafe practices such as kissing or cuddling chickens have increased in Vermont. Overall, the data indicate the need for improved messaging on biosecurity and risks associated with backyard chickens

DeCicco, M., Larsen, K.M., Hood, K., Etter, A.J. Salmonella enterica Frequency in Backyard Chickens in Vermont and Biosecurity Knowledge and Practices of Owners.

We’ll post a non-technical abstract at some point soon.

~Andrea Etter

2022 Samplings Have Started!

We are several weeks into our 2022 chick sampling and have so far we have processed 23 samples. We have found several positive so far, so we’re keeping an eye on things to see what happens! Of course, the vast majority of chick days are still to come, so it’s too soon to know if this year will be better or worse for Salmonella rates.

Sequencing of last year’s isolates is also in process, so we should soon start finding out what types of Salmonella the chicks and chickens from last year were infected. Why is this important? Not all types of Salmonella are likely to cause human illness. We’ll also be able to learn from the sequences whether or not these Salmonella have resistance to antibiotics and, if so, if they are resistant to medically-important antibiotics like Ampicillin. Stay tuned!

Upcoming Webinar (3/14) on Salmonella on backyard chickens

As we’re heading towards the sampling season, we’re partnering with Sugar Feather Farm to present a webinar on our research on Salmonella and chickens/chicks and what that means for backyard chicken owners.

To sign up, click the link below. It’ll ensure you get a calendar invite and an email reminder about the webinar the day before.

When: Mar 14, 2022 07:00 PM Eastern Time (US and Canada)

Topic: Chicks, Chickens, and Salmonella–oh my!

Register in advance for this webinar:…/reg…/WN_tXroKhI2S0iD9dG7avntTA

After registering, you will receive a confirmation email containing information about joining the webinar.

December Roundup & Planning for Next Season

We’re nearly done with processing all this year’s samples. Some turnover in lab members has led to some sample data getting lost & samples needing to be reprocessed (ugh!). But such is life. The team is now solidified and fully trained, so we’re making good progress & will hopefully close out the 2021 samples prior to the end of 2021 \_(._.)_/

We’re also planning next year’s sampling and trying to build organizational systems that accommodate the high number of samples that we’ll hopefully get. Last year proved we needed these systems; this year we plan to have them in place. Live and learn?

A major goal for next sampling season is to get more adult backyard chicken flocks enrolled and sampled. We sampled 28 in our first year (2019), but only 10 in 2020 and about the same number this past year. I’d like to get another 30 this year (2022). We shall see. Our work relies on (1) people volunteering their flocks and (2) having students who are able to help advertise and drive the project, so it’s tricky. I think I have #2 covered, but the sampling schedule with the chicks from March-June also tends to distract from the adult BYC effort.

Interested in volunteering your flock?

email me at and reference “BYC-VT” or “Backyard chickens”

Research Update: October 12, 2021


We’ve added a few more chickens/flocks to our roster since July. We’re now up to 41 flocks (40 hobby flocks). Of these, five have had chickens with Salmonella, with a total of six chickens of 430 having Salmonella.

What does this mean?

  • The odds of an individual chicken having Salmonella are pretty low–about 1/100.
  • The odds of a flock having a chicken with Salmonella are fairly high–about 12% of flocks have at least one chicken with Salmonella.


We have gotten though 211 chick bedding samples since March 2020. We have done 135 this year, and we still have about 65 in the freezer. So far, we have found 35 total chick bedding samples positive for Salmonella (34 this year). Of these, 75% come from hatcheries participating in the National Poultry Improvement Plan for reducing Salmonella. You can also see that we’re finding a lot more Salmonella this year, overall.

We do collect data by hatchery, and we also found a lot of variation by hatchery. Our non-NPIP hatchery had the lowest positivity rate (16% of chick bedding pads contained Salmonella). In one of our NPIP hatcheries, 79% of the chick shipping pads tested positive for Salmonella (in the other, only 21% of pads had Salmonella).

What does this mean?

  • This may be a high Salmonella year. Or last year might have been low. Or it might be a difference in where we’re sampling. There are, unfortunately, a lot of possibilities. We’ll know more next year.
  • NPIP isn’t working well this year. This may be due to COVID difficulties (inability to get USDA staff people out to monitor hatcheries, etc). It could also be that hatcheries cut corners this year to meet demand (especially after last year) and the USDA hasn’t clamped down on this yet. It’ll be interesting to see what we find next year.
  • Looking at trends over time is really important for drawing robust conclusions–last year, it looked like NPIP was really working well. This year, I wouldn’t spend the extra $1.50/bird on an NPIP-certified hatchery chick.
  • There is a lot of variation in Salmonella rates among hatcheries.
  • Salmonella-monitoreddoesn’t mean “Salmonella free” when it comes to chicks from NPIP-participating hatcheries
  • Not kissing your chicks and washing hands after handling your chicks are your best bets for avoiding extra time on the toilet.
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Research Update 7/22/2021

Chicks and Salmonella update

Sorry it’s been a while. We had a contaminated pipette shedding Salmonella into our samples, so we were delayed while we switched out pipettes, cleaned everything, implemented more stringent controls, and re-ran all our positive samples (we almost always collect more sample than we need and have the extra frozen).So here we are, in the third week of July, with nearly all the summer’s samples collected, and having run 177 samples since March 2020, while more than 90 samples remain in our freezers waiting to be run.

We have 16 PCR-confirmed positives out of 177 samples, for an all-time total of 9.0% of chicks positive for Salmonella. Of these, 7/89 come from NPIP-certified hatcheries, while 9/59 come from non-NPIP certified hatcheries. Another 29 samples came from individuals, with unknown sourcing.

So what does this mean?

  • Almost 10% of all chick shipments are positive for Salmonella. This isn’t terrible, but it’s not great.
  • The numbers for just this year’s samples are worse, with 15.5% of samples positive for Salmonella. This may be due to study design vs an increase in Salmonella-positive chicks.
  • Chicks from non-NPIP hatcheries are roughly 2x as likely to contain Salmonella.
  • NPIP certification does not appear to be entirely solving the problem. This may be in part because ag stores don’t always use the same hatchery year to year; if they re-use equipment from a hatch/shipment with Salmonella, there is a risk of passing it on to the new chicks. I’ve reached out to NPIP representatives to get a better idea of what the expected rate of Salmonella would be in NPIP-certified flocks, but no response yet.
  • Store setup matters; leaving chicks in open pens is a greater risk to both the customers and the chicks. It’s better to leave chicks inaccessible to customers. Cleaning between shipments is also vital.

What can you do about this?

  • Assume your chicks could have Salmonella
  • Don’t kiss your chicks or hold them near your face. Chicks are messy creatures and may have fecal material on their feathers. Feces can be extremely Salmonella-rich (besides being gross)
  • Supervise kids around chicks. It’s ok to pet them, but kids should wash their hands afterwards
  • Wash your hands after cleaning chick pens or waterers and don’t clean out your chick equipment in the kitchen sink (bathtub is a better choice)

Research Updates 5/18/21: Adult chickens; babies

Chicken sampling, 2019 (image by Rachel Leslie, UVM)

The last couple of weeks have been exciting for chicken & chick sampling results. Keep in mind that “exciting” for scientists is roughly the same as “interesting times,” in this case meaning we have found a lot of Salmonella recently.

ADULT BIRDS: We have found Salmonella in an additional flock of chickens, bring our adult bird totals up to 4/403 birds positive, and 3/31 flock positive (see chart below).

Salmonella percent positives as of 5/18/2021

What does this mean for Vermont BYC owners?

  • The bad news: Salmonella is 3x more common in Vermont flocks of chickens (10%; 3/31 flocks) than it is in western WA (3%; 1/34 flocks) or in the greater Boston area (1.9%; 1/53 flocks). Possible reasons for this difference includes a higher number of rural flocks in our study than in the WA and Boston studies (the Boston study was entirely urban). Wild birds, rodents, and mammals can all have Salmonella, and they can pass it on to backyard chickens, and our Salmonella-positive flocks have all been from rural farms/homes.
  • The good news: looking at by-bird rates, Salmonella is extremely rare in chickens in Vermont, with fewer than 1% of chickens testing positive
  • Other good news: In the flocks we tested, only one or two of the birds in each flock had Salmonella at the time we tested. This means that you do not have to cull your whole flock if one has/gets Salmonella

CHICKS: We have found our first positive samples from chicks purchased from flocks participating in NPIP. No system is perfect, but this is a bit concerning nonetheless.

Hatchling Samples & Positives (5/18/2021)

What does this mean for Vermonters buying baby chicks?

  • More than half our samples have come from NPIP-certified hatcheries, which are expected to be Salmonella-free
  • 10/69 samples not from NPIP-certified hatcheries were positive (15%).
  • 4/81 samples from sellers purchasing from NPIP-certified hatcheries were positive (5%)
  • Overall, more than 7% of the chick pens/shipments we’ve sampled contain Salmonella, indicating that baby chicks often carry Salmonella
  • Takeaway: Buying from an NPIP-certified hatchery or a store that buys from an NPIP-certified hatchery is the best way to reduce your risk of catching Salmonella from baby poultry, but you should still be careful about kissing or cuddling your baby chicks as no system is 100% sure.

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