Urine sample collection is common procedure. It requires utmost care that there is no contamination of urine with other bacteria.

It is important to collect clean catch midstream urine sample after cleaning the genitals of the child with only water or along with mild soap.

Clean catch means that the urine directly enters the container. It does not drip into the container after falling on other contaminated surface. 

Midstream sample would mean that the the urine is collected in the middle of the stream, minimizing the chance of contamination from the initial and final parts of urination.

It is easier in toliet trained children but in smaller children urination can be induced by slight pressure in lower belly or my massaging this area with cotton dipped in cold water.