It seems to be a natural part of our environment and our microbiom, so finding it in stool may not mean anything unusual.
It is natural part of stool of both humans and animals, but there seem to be strains that may be more problematic.
C. freundii is a soil organism, but can also be found in water, sewage, food and in the intestinal tracts of animals and humans. The Citrobacter genus was discovered in 1932 by Werkman and Gillen. Cultures of C. freundii were isolated and identified in the same year from soil extracts.
C. freundii is a common component of the gut microbiome of healthy humans. While most strains are beneficial, there are significant phenotypic variations among strains, even those that share >99% of their genome. Some rare strains of C. freundii have been associated with opportunisitic nosocomial infections of the respiratory tract, urinary tract, blood, and many other normally sterile sites in immunocompromised patients.