22Antimicrobial resistance (AMR) in drinking water has received less attention than 23 counterparts in the urban water cycle. While culture-based techniques or gene-centric 24 PCR have been used to probe the impact of treatment approaches (e.g., disinfection) on 25 AMR in drinking water, to our knowledge there is no systematic comparison of AMR 26 traits between disinfected and disinfectant residual-free drinking water systems. We use 27 metagenomics to assess the associations between disinfectant residuals and AMR 28 prevalence and its host association in full-scale drinking water distribution systems 29 (DWDSs). The differences in AMR profiles between DWDSs are associated with the 30 presence or absence of disinfectant. Further, AMR genes and mechanisms enriched in 31 disinfected systems are associated with drug classes primarily linked to nontuberculous 32 mycobacteria (NTM). Finally, evaluation of metagenome assembled genomes (MAGs) 33 of NTM indicates that they possess AMR genes conferring intrinsic resistance to key 34 antibiotics, whereas such NTM genomes were not detected in disinfectant residual free 35DWDSs. Thus, disinfection may not only influence the AMR profiles of the drinking 36 water microbiome but also select for NTM with intrinsic AMR. 37 38 39 Regulation compliant drinking water can contain low concentrations of chemicals and 41 microorganisms originating from source water, treatment process, distribution systems, 42 and premises plumbing 1,2 . While our understanding of chemical contaminants (e.g., 43 disinfection by-products (DBP) 3 ) and microbial populations 4-6 in treated drinking water 44 is increasing, the drinking water field has only recently started investigating emerging 45 biological contaminants 7 like antibiotic resistance bacteria (ARB) and antibiotic 46 resistance genes (ARG). Misuse of antibiotics and anthropogenic release of bioactive 47 compounds into the urban water cycle exacerbate the prevalence and persistence of 48 antimicrobial resistance (AMR) and can make engineered systems for water treatment 49 (i.e., wastewater and drinking water) critical points of AMR dissemination 8,9 . Drinking 50 water can constitute a potential exposure route to microorganisms with intrinsic and 51 acquired antibiotic resistance genes (i.e., resistome 10 ), and it is particularly concerning 52 if AMR traits are associated with waterborne pathogens 11 . 53
54Drinking water disinfection is one of the most important public health advances towards 55 elimination of waterborne diseases and remains the most widely used treatment strategy 56 today for pathogen control 12 . Typically, drinking water systems (DWS) maintain a 57 disinfectant residual, usually chlorine, in the drinking water distribution system 58 (DWDS) to minimize microbial growth. However, its unintended impacts (e.g., DBP 59 formation) have prompted the evaluation of alternative strategies to mitigate associated 60 risks. These range from the use of alternate disinfectants such as chloramines, to 61 advanced oxidation processes th...