Baby got urine infection!!!?

when my son was one week old he was taken into hospital because he was projectile vomiting (they never found a reason why he was vomiting but it has stopped now) anyway they took a routine urine sample from him and did a culture test on it. something grew in the sample so they phoned me and asked me to fetch him back in to take another sample because the bacteria that was found in the urine is a bacteria that we all have in our stools so they were unsure weather or not it had got mixed in with the urine. anyway the second sample came back positive with the same bacteria meaning he had a uti. the doctor said this does happen but is very uncommon and now they are wanting to do test on his kidneys to check for abnormalities and damage. im very worried i am wondering if anyone has had the same happen to someone they know if so could you please share and let me no what it was. also if anyone knows why babys so young get uti's please share too thank you