Prospective genomic surveillance reveals insights into antimicrobial resistance and lineage diversity of uropathogen in older adults in Queensland

Community-acquired urinary tract infections (UTIs) are a significant health concern in older adults. Few studies have investigated uropathogen epidemiology across diverse settings where older adults reside. In this study, we prospectively collected and whole genome sequenced urinary isolates of Escherichia coli, Klebsiella species, and Enterobacter cloacae complex from individuals aged 70 and over living in the community and residential aged care facilities (RACFs) settings in Queensland. The prevalence of antimicrobial resistance, pathogen population structure and transmission dynamics across the settings were investigated. E. coli was the most commonly identified species (82.2%, 447/544), followed by K. pneumoniae (10.8%, 59/544) and E. hormaechei (2.6%, 14/544). Intra-species lineages were diverse with a total of 177 sequence types being identified. The three predominant lineages were E. coli ST73 (10.7%, 54/504), ST95 (8.1%, 41/504) and ST131 (5.4%, 27/504). Transmission events were minimal, being identified in 13 patients (2.5%) mainly from the community. Resistance rate to antibiotics were low with small proportion (9.7%) of multidrug-resistant (MDR) isolates. The predominant MDR lineage was E. coli ST131 carrying extended-spectrum beta-lactamase (ESBL) blaCTX-M genes. Community-acquired UTIs in older adults are predominantly caused by diverse E. coli lineages, without much evidence of transmission within aged care facilities. The low rates of antimicrobial resistance in the community and absence of strains adapted to a particular setting suggest that current empiric therapy guidelines remain appropriate. Our prospective genomic surveillance provides valuable insights for monitoring UTIs in this population and demonstrates the importance unbiased approach to accurately capture the prevalence and diversity of uropathogen lineages.