The ARB and ARG can be found in many more environmental samples than you mention. " Increased levels of antibiotic resistant bacteria in the environment may have different causes. It could be a consequence of on-site selection from antibiotic residues in the environment, hence promoting the evolution of new forms of resistance. Alternatively, it is simply due contamination by fecal bacteria that often tend to be more resistant than other bacteria." Article Fecal pollution can explain antibiotic resistance gene abund...
But to your question:
According to my opinion antibiotic resistant bacteria and genes are not direct water treatment problem, as far as I know.
Exposure to antibiotics, which is prevalent in antibiotic usage, excretion, and disposal (especially in wastewater and its return to the environment, even after treatment), selects for antibiotic resistance. In other words, it kills off organisms that are susceptible and, therefore, increases the population of antibiotic resistant organisms in the long run.
Furthermore, antibiotic resistance can be acquired by originally non-resistant organisms by horizontal gene transfer because most antibiotic resistance genes (ARGs) are located on plasmids that are exchanged between organisms.