IPPE: Environmental surveillance reveals hidden microbial risks in hatcheries

20 May 2026

5 minute read

By: Sarah Mikesell

South America

North America

Dr. Joshua Deines, technical service device lead at Zoetis, spoke to The Poultry Site’s Sarah Mikesell at IPPE in Atlanta, Georgia, USA about new study data looking at microbial loads at hatcheries to identify areas that can often be contaminated.

Why is environmental and microbial surveillance such a critical component of hatchery sanitation? 

We want to see what challenges we currently have in a facility – what’s around it and what inputs are coming in. We think of all our bacterial and fungal load, and they come from one of four things: eggs, water, people or air. We're trying to sample all those and see how they enter the facility and what we're dealing with so that we can create a sanitation program. Once we have a sanitation program, those surveys confirm its effectiveness and what needs to be improved, and ultimately move the needle to help improve chick health. 

This study evaluated microbial loads across many hatchery areas from egg rooms to in ovo vaccination rooms. What was the goal of surveying such a broad range of locations? 

Every piece of the hatchery has an impact, but they're all going to be impactful in different ways. We try to break it down into segments of the hatchery, and we've been doing this survey for many years. 

This study collected a portion of those from last year to do a comparison and look at which areas these problems stem from. If we can look at different areas, we can focus better on an action plan for how to clean those up and target the areas that are most likely to cause a problem with chick health. For example, the setters or the laboratory for vaccine mixing are hot areas, and this study confirmed that they often are overburdened and are a place that we need to focus. 

What were the most significant findings from the study, particularly regarding Aspergillus and bacterial contamination across facilities? 

Of the nine hatcheries in this study, Aspergillus was discovered in at least six of those hatcheries across multiple locations. Even though Aspergillus has been on people's radar for a long time – it’s well published and well studied – we know it can cause problems for chick health in the hatchery. Even though we've been trying to tackle it, it still persists. Maybe we're not looking at it the right way or pushing hard enough. Or the burden of the incoming challenge is just so strong that our current practices just aren’t fighting it off. 

We found a lot of Aspergillus, especially in concerning areas; it's coming in both on the eggs and in the air. At a lot of the hatcheries, we do roof plating and sample the air. People always think, “well, that's not really the hatchery,” but we also want to know about environmental challenges outside of the hatchery. So, what is knocking at our door that we need to fend off?  

A lot of hatcheries had Aspergillus on the egg packs that came into the facility. That tells us the breeder flocks have it, so it’s recurring and coming into the hatchery all the time. We can’t afford to take a break from fighting it off. It's when it gets to the end, at hatching time, that it's most problematic, so targeting it head-on is essential.

Were the study results surprising?

Yes, we know that Aspergillus can be a problem and it's been around for some time, but people are always so focused on it that we assume that it’s not a problem and is more of a background concern, especially if we're not seeing it in the chicks. We just assume that it's not there. Many times, it's close to being a problem and then it just takes a few more things to go wrong or the chicks to be stressed in another way for it to explode. 

We've also had a lot of products that have been effective for controlling fungal challenges that are now off the market and with regulation, are now hard to get. We're having to find other products and other ways to control Aspergillus.

Were there specific areas within hatcheries that were more frequently contaminated, and why were these locations especially important to address? 

Two places in this particular study that were highlighted were the laboratory, where we’re mixing and preparing vaccines, which really should be one of the cleanest places in the facility because that's what we're injecting into an embryo. Any contamination is going to be incubated and potentially pathogenic and problematic for the embryo. The lab should be really clean and was definitely not. 

The other location that we highlighted was in the setters. This happened for a few reasons, but one is that the setter is harder to clean than the lab, especially if you're in a multi-stage incubator hatchery. It’s not all-in-all-out. The opportunity to get in and do a deep clean is very rare. That wasn't necessarily surprising but shows that our embryos are having a challenge against them during incubation. 

The lab was most surprising, similar to the Aspergillus, because we know it should be a focal point, but are we really adhering to the sanitation practices that we think we have in place or are those sanitation practices not working. 

How can routine environmental surveys help hatcheries move beyond general cleaning towards more targeted improvements in sanitation and biosecurity protocols? 

The two key factors are routine and targeted. Many people don't do any sampling until it's already too late, and problems are already present. If we're doing routine surveys, it confirms if our sanitation program is working or not. Take samples after cleaning and see if they’re truly clean. Do it before there’s a problem.

Targeted sampling is the second part. If we just sample randomly, you're not focusing. If you target a specific location that is higher risk, like the lab, that's the place you should focus first because it's going to make the biggest impact. Once you tackle that, you can move on to other things because it can be intimidating to try to look at a whole hatchery program. So, if you can break it down by area -- what's most important? Learn from that and then go to the other areas. 

How can improving chick cleanliness and critical hatchery areas translate into better chick livability, feed conversion and overall flock health? 

The hatchery is the start of life for the chick. If we think about a broiler and its average age at processing, it will spend one-third of its life in the hatchery as an embryo. We often don't think about that whole timeline and how your chick quality at the hatchery is a clear indicator of what your predicted seven-day livability and feed conversion ratio are like. So, if they start with good, sealed navels, no yolk infections and no Aspergillus challenge, they're going to be healthier when they get to the field. It’s all about managing your sanitation at the hatchery.