Global prevalence of colistin resistance, mcr gene variants, and sequence types in Pseudomonas aeruginosa, Klebsiella pneumoniae, Escherichia coli, and Stenotrophomonas maltophilia: a systematic review and meta-analysis

Abstract

Abstract Background Due to the increasing prevalence of infections caused by multidrug-resistant (MDR) Gram-negative bacteria, colistin has become an important therapeutic option. However, the rapid emergence of resistance to this antimicrobial agent, mediated by mechanisms such as lipopolysaccharide (LPS) modification and plasmid-borne mcr genes, has emerged as a major global health concern. This systematic review and meta-analysis aimed to estimate the global prevalence of colistin resistance among clinically important Gram-negative bacteria, including Escherichia coli ( E. coli ), Klebsiella pneumoniae ( K. pneumoniae ), Pseudomonas aeruginosa ( P. aeruginosa ), and Stenotrophomonas maltophilia ( S. maltophilia ), identify their sequence types (STs), and characterize the distribution of mcr variants. Methods A comprehensive literature search was conducted in three databases (PubMed, Embase, and Web of Science) to identify English-language publications published between 2000 and 2025, following the PRISMA guidelines. Eligible studies reported the prevalence of colistin resistance among clinical isolates of the four target bacterial species. Pooled prevalence estimates with 95% confidence intervals (CIs) were calculated using random-effects meta-analysis in Stata version 18. Subgroup analyses were performed according to continent, publication year, and colistin resistance detection method. Results A total of 245 studies met the inclusion criteria, including P. aeruginosa ( n = 89), K. pneumoniae ( n = 106), E. coli ( n = 42), and S. maltophilia ( n = 8). The pooled global prevalence of colistin resistance was 5.9% for P. aeruginosa , 20.6% for K. pneumoniae , 4.0% for E. coli , and 38.5% for S. maltophilia . At the country level, higher prevalence estimates were observed for P. aeruginosa in Canada, India, and Spain; for K. pneumoniae in Brazil and Greece; for E. coli in China and Turkey; and for S. maltophilia in countries with available but limited data, including Colombia, Thailand and Hungary. The most frequently identified STs were ST235 in P. aeruginosa (58.0%), ST101 in K. pneumoniae (29.0%), and ST131/ST69 in E. coli (10.6% each). The predominant colistin resistance gene was mcr-1 , accounting for 100% of resistant P. aeruginosa , 57.4% of resistant K. pneumoniae , and 97.8% of resistant E. coli isolates, whereas no mcr variants were reported in S. maltophilia . Conclusion Colistin resistance remains a significant and expanding threat among major Gram-negative pathogens worldwide, with substantial geographical variation in resistance prevalence, ST distribution, and mcr gene profiles. The scarcity of data from certain regions, particularly Oceania, and the limited number of studies conducted in several countries highlight critical gaps in global surveillance. The high resistance rates observed in some regions emphasize the urgent need for coordinated international surveillance, antimicrobial stewardship programs, and targeted infection control strategies to limit the dissemination of colistin-resistant strains.