From Table 2, it can also be seen that there was a relatively high reduction in carbapenemase genes and 16S rRNA genes in SCT, where the removal efficiency of these genes was higher than 99%. There were approximately 2 orders of magnitude reductions in carbapenemase genes in SCT compared with AeT. High concentrations of carbapenemase genes were settled and transferred into sludge, which increases the risk of propagating carbapenemase genes to endogenous soil bacteria through sludge disposal. Moreover, the removal efficiency for total bacteria (assessed by 16S rRNA genes) through chlorination disinfection was higher (p < 0.05) than bacteria harboring carbapenemase genes. The removal efficiency for 16S rRNA gene by chlorination was 90.5 ± 7.5% versus 52.4 ± 4.1% for blaKPC-2, 12.9 ± 2.8% for blaGES-1, and 4 ± 0.3% for blaIMP-1. This finding suggests that some bacteria harboring antibiotic resistance genes may be co-resistant to chlorination, as suggested by previous research [42,43]. However, resistance to chlorination is unlikely to be mechanistically related to antibiotic resistance. Disinfection is often thought to destroy most pathogens in WWTP effluents, and chlorination is the most common treatment used as compared to ultraviolet (UV) or ozonation disinfection. However, the results of this study showed that disinfection by chlorination could not achieve a significant reduction of carbapenemase genes in the WWTP, which is also consistent with previous research on tet-ARGs [44]. Although the abundance of carbapenemase genes were reduced somewhat through the WWTP, the continuous discharge from the WWTPs was still a potential route of carbapenemase genes into the environment.