Extracting novel antimicrobial emergence events from scientific literature and medical reports

Despite considerable global surveillance of antimicrobial resistance (AMR), data on the global emergence of new resistance genotypes in bacteria has not been systematically compiled. We conducted a study of English-language scientific literature (2006-2017) and disease surveillance reports (1994-2017) to identify novel global emergence events (first clinical reports of unique drug-bacteria resistance combinations). We screened 24,966 abstracts and reports, ultimately identifying 1,773 novel emergence events from 294 articles. Events were reported in 66 countries, with most events in the United States (152), India (129), and China (128). The most common bacteria demonstrating new resistance were Klebsiella pneumoniae (352) and Escherichia coli (218). Resistance was most common against antibiotic drugs Imipenem (89 events), Ciprofloxacin (85) and Ceftazidime (82). We provide an open-access database of emergence events with standardized fields for bacterial species, drugs, location, and date, and we discuss guidelines and caveats for data analysis. This database may be broadly useful for understanding rates and patterns of AMR evolution, identifying global drivers and correlates, and targeting key surveillance and interventions.