Colistin-resistant Klebsiella pneumoniae species complex: The scenario in Mexico

• Comprehensive analysis of colistin-resistance mechanisms. • Genomic surveillance of colistin-resistant Klebsiella pneumoniae in Mexico. • NDM-1 is far more prevalent than KPC-type carbapenemases in Mexico. • Required approval and introduction of cefiderocol and aztreonam-avibactam to expand the available options beyond colistin. • Hypervirulence and colistin resistance coexist Characterize the colistin-resistance mechanisms, determine the molecular epidemiology, and genomic traits of the colistin-resistant Klebsiella pneumoniae species complex (ColR-KpSC) clinical isolates in Mexico. In this study, 1,539 KpSC isolates were collected in Mexico from 2016 to 2021. We conducted a comprehensive analysis that included microbiological, genetic, molecular, and genomic approaches. A total of 50 isolates (3.25%) were colistin-resistant; of which 49 (98%) corresponded to K. pneumoniae and 1 (2%) to Klebsiella quasipneumoniae . Whole genome sequencing of these resistant isolates revealed intra- and inter-hospital dissemination, and the mgrB inactivation was the main resistance mechanism. Some KpSC isolates carried plasmid-borne mcr-1 gene found in Escherichia coli from piglets in Mexico. The colistin-resistant isolates presented a high prevalence of ESBL- and NDM-1 genes, and one hypervirulent strain also produced ESBL CTX-M-15. This study provides a comprehensive snapshot of the epidemiology of ColR-KpSC in Mexico, highlighting a high prevalence of NDM-1 carbapenemase among ColR-KpSC isolates; this is in line with previous reports identifying NDM-1 as the most prevalent carbapenemase in K. pneumoniae species complex. This problem is particularly concerning in Mexico because of the lack of therapeutic options.