Establishing Antimicrobial Resistance Surveillance in the Water and Environment Sector in a Resource-Limited Setting: Methodical Qualitative and Quantitative Description of Uganda’s Experience From 2021 to 2023

Abstract

Background Antimicrobial irrational use and poor disposal in the human and animal sectors promote antimicrobial resistance (AMR) in the environment as these antimicrobials and their active ingredients, coupled with resistant microbes, are released into the environment. While AMR containment programs in the human and animal sectors are well established in Uganda, those in the water and environment sector still need to be established and strengthened. Therefore, the Ministry of Water and Environment set out to establish an AMR surveillance program to bolster the One Health efforts for the containment of AMR under the National Action Plan 2018-2023. Objective This study aims to describe Uganda’s experience in establishing AMR surveillance in the water and environment sector. Methods A methodical qualitative and quantitative description of the steps undertaken between August 2021 and March 2023 to establish an AMR surveillance system in the water and environment sector is provided. The Uganda Ministry of Water and Environment used a stepwise approach. Governance structures were streamlined, and sector-specific AMR surveillance guiding documents were developed, pretested, and rolled out. The National Water Quality Reference Laboratory infrastructure and microbiology capacity were enhanced to aid AMR detection and surveillance using conventional culture-based methods. A passive and targeted active surveillance hybrid was used to generate AMR data. Passive surveillance used remnants of water samples collected routinely for water quality monitoring while targeted active surveys were done at selected sites around the Kampala and Wakiso districts. Excel and Stata 15 statistical software were used for data analysis. Results A sector-specific technical working group of 10 members and focal persons is in place, providing strategic direction and linkage to the national AMR surveillance program. The National Water Quality Reference Laboratory is now at biosafety level 2 and conducting microbiology testing using conventional culture-based techniques. Up to 460 water samples were processed and 602 bacterial isolates were recovered, of which 399 (66.3%) and 203 (33.7%) were priority pathogens and nonpriority pathogens, respectively. Of the 399 priority pathogens, 156 (39.1%), 140 (35.1%), 96 (24.1%), and 7 (1.8%) were Escherichia coli, Klebsiella species, Enterococcus species, and Salmonella species, respectively. E coli showed resistance to ampicillin (79%), ciprofloxacin (29%), and ceftriaxone (29%). Similarly, Klebsiella species showed resistance to ampicillin (100%), ciprofloxacin (17%), and ceftriaxone (18%). Enterococcus species showed resistance to ciprofloxacin (52%), vancomycin (45%), and erythromycin (56%). Up to 254 (63.7%) of the priority pathogens recovered exhibited multiple and extensive resistance to the different antibiotics set. Conclusions Initial efforts to establish and implement AMR surveillance in the water and environment sector have succeeded in streamlining governance and laboratory systems to generate AMR data using conventional culture-based methods.