The word "Cooties", in the World War One sense of the word, were tiny little bugs that lived in the seams of uniforms for that unlucky multitude who lived in the trenches. Being an equal-opportunity sort of parasite, they plagued all combatants alike, regardless of one's opinions concerning Belgian neutrality, and were cause for much complaining, scratching, discomfort and the creation of way too much juvenile verse.
The attached article from 1917 tells the tale of some fortunate Doughboys and their encounter with a U.S. Army "Cootie Graveyard" (read: delousing station):
"They entered a bedraggled, dirty, grouchy lot of sorry-looking Doughboys. They came out with faces shinning and spirits new. They knew they had before them the first good night's rest in some time and sans scratching."
As far as cooties were concerned, the American infantrymen of the Great War had it far easier than his European comrades and counter-parts, for he only had to contend with them for the mere six month time that he lived in the trenches, rather than the full four years.
More articles about W.W. I trench warfare can be read here.