During El Niño events, heavy rainfall or prolonged drought alter housing microclimates, affecting disease risks differently in open-sided and closed poultry houses.

In open-sided houses, heavy rainfall increases litter moisture and ammonia levels, promoting coccidiosis and pododermatitis. Dry conditions increase airborne dust, irritating the respiratory tract and increasing the incidence of colibacillosis.

Closed houses with mechanical ventilation can better control humidity; however, power outages during storms can lead to rapid ammonia buildup. During drought, air recirculation may concentrate pathogens, increasing the risk of viral respiratory diseases.

To mitigate these risks, in open houses during wet periods, litter turning should be increased and ridge ventilation should be installed. During dry periods, misting systems can be used to reduce dust levels. For closed houses, backup generators and ammonia sensors integrated with exhaust fan control systems are recommended. Cleaning schedules should also be adjusted based on rainfall forecasts. These targeted measures can reduce disease incidence under El Niño extremes.

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