The effect of pregnancy on inflammatory bowel disease (IBD) remains poorly understood. We aimed to monitor intestinal inflammation using fecal calprotectin (FC) in pregnant women and their babies during early life.
Pregnant women with or without IBD and their infants were prospectively enrolled. FC levels were measured at each trimester of pregnancy and in babies throughout the first 3 years of life. Repeated measures analysis was applied to investigate changes in FC levels while adjusting for confounders. The FC levels were correlated with the bacterial abundance in both mothers and babies.
614 fecal samples from 358 mothers (98 with IBD) and 1,005 fecal samples from 289 infants (76 born to IBD mothers) were analysed. Pregnant IBD patients maintained higher FC levels through pregnancy as compared to controls (p=7.5×10). FC gradually increased in controls and declined in IBD patients throughout pregnancy (p for interaction=5.8×10). Babies born to IBD mothers presented with significantly higher FC levels than those born to controls up to 3 years of age, after adjusting for sex, delivery mode, feeding behaviour and antibiotics exposure (2 weeks to 3 months of age p=0.015, 12 months to 36 months of age p=0.00003). Subdoligranulum, Roseburia, Fusicatenibacter and Alistipes negatively correlated, while Streptococcus, Prevotella, Escherichia-Shigella, and Bifidobacterium positively correlated with maternal FC levels at T3. Faecalibacterium, Bifidobacterium and Alistipes showed negative correlations, while Streptococcus were positively correlated with FC levels within 3 months of birth.
Pregnancy is associated with decreased inflammatory activity in mothers with IBD. Higher FC levels in babies born to IBD mothers suggest subclinical inflammation in early life whose long-term consequences are uncertain.

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