Prevalence of and risk factors for antimicrobial resistance in pneumococcal disease in southern Ontario during the PCV13 era

BACKGROUND: Pneumococcal infections are an important cause of morbidity and mortality, and a major contributor to the burden of antimicrobial resistance (AMR). Multiple factors affect AMR in pneumococci. METHODS: The Toronto Invasive Bacterial Diseases Network (TIBDN) conducted population-based surveillance for invasive pneumococcal disease (IPD) and hospitalization due to non-bacteremic pneumococcal pneumonia (NBPP) in Toronto/Peel Region, Ontario. Laboratories reported sterile site and respiratory isolates of Streptococcus pneumoniae. Patient data were collected by chart review and patient/physician interview. Population data were from Statistics Canada. Antimicrobial susceptibility testing was performed/interpreted per Clinical and Laboratory Standards Institute guidelines and/or by prediction from whole genome sequencing (WGS). Serotyping was performed by Quellung reaction or WGS. RESULTS: From 2014 to 2024, 3881 episodes of IPD and 887 of NBPP were identified. Resistance was most common to macrolides (31.4%, 1285/4086), tetracyclines (17.4%, 653/3756), penicillin (meningeal breakpoints: 17.2%, 749/4354), clindamycin (12.3%, 472/3823) and trimethoprim-sulfamethoxazole (12.6%, 495/3929); resistance to ceftriaxone (meningeal breakpoints) and levofloxacin was