You can suspect bad bacteria is present but not tell, a culture test as far as I'm aware is the only way of finding out for sure. I would suspect bad bacteria if a pigeon show any of the following signs, limping, swollen joints, poor performance, loose droppings, dull in appearance. Again as far as I'm aware bad bacteria is ever present in pigeons and is always probing for a weakness trying to take a foothold somewhere. I'll give you an example. A good few years back I had a team of young birds that were underperforming, something wasn't right so I sent of 3 youngsters to a vet with instructions to find out what the problem was even if it meant culling them and carrying out tests on stomach, organs etc. Cultures were done on blood & organs and the findings were bacteria was present around their hearts! giving the heart a swollen flabby appearance, consequently the pigeons couldn't perform nowhere near their best. In this case the pigeons looked in all respects healthy but it was the poor performance that got the alarm bells ringing.