Some fungi, particularly those that cause root and stem diseases, have specialized spores that can survive many years in the soil in the absence of squash. Bacteria are smaller than fungi and are not at all plant-like. All bacteria are just one cell, and they lack chlorophyll. The ones that cause plant disease do not form spores. The major type of reproduction for plant pathogenic bacteria is by simple cell division.
Bacteria never enter plants directly.
They must have a wound or a natural opening to get inside a potential host plant. There are no cellular structures. New virus particles can only be reproduced inside of living cells. They are much smaller than bacteria, and normally require sophisticated techniques such as electron microscopes and polymerase chain reaction to be studied. Viruses probably spread from infected weed hosts to squash.